Contacts of the helix formed by residues 617 - 641 (chain B) in PDB entry 6R7X
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with PRO 617 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B ARG* 3.7 45.8 - - + +
266B ALA* 3.9 12.8 - - + -
267B ASN* 4.7 6.1 - - + -
614B PRO* 5.9 1.3 - - - -
615B ASP 4.2 1.1 - - - +
616B LYS* 1.3 92.2 - - + +
618B ARG* 1.3 65.4 + - - +
619B HIS* 3.6 20.6 - - + -
620B ILE* 3.8 24.2 - - + -
621B GLN* 3.3 21.0 + - - +
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Residues in contact with ARG 618 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A SER* 5.7 3.2 + - - -
310A ARG* 5.7 4.4 - - - +
263B ARG* 4.7 4.6 - - - +
617B PRO* 1.3 75.9 - - - +
619B HIS* 1.3 61.5 + - - +
621B GLN* 3.2 22.2 + - - +
622B MET* 2.9 53.9 + - + +
907B UMQ 4.9 19.5 + - - +
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Residues in contact with HIS 619 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B ASN* 4.1 13.8 + - - -
617B PRO* 4.1 20.5 - - + +
618B ARG* 1.3 78.2 + - - +
620B ILE* 1.3 89.4 + - + +
622B MET* 3.4 19.2 + - + +
623B LYS* 2.9 53.8 + - - +
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Residues in contact with ILE 620 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B ALA 4.3 3.6 - - - +
267B ASN* 3.8 19.1 - - - +
270B TYR* 3.6 48.7 - - + -
275B LEU* 4.1 15.7 - - + -
616B LYS* 4.9 6.7 - - + -
617B PRO* 3.8 31.1 + - + -
618B ARG 3.3 0.2 - - - -
619B HIS* 1.3 102.5 - - + +
621B GLN* 1.3 57.8 + - - +
623B LYS* 3.3 6.6 + - + +
624B LEU* 2.9 37.5 + - + +
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Residues in contact with GLN 621 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614B PRO* 5.1 7.1 - - - +
616B LYS* 4.4 21.7 - - + +
617B PRO 3.3 18.7 + - - +
618B ARG* 3.2 22.2 + - - +
620B ILE* 1.3 79.4 - - - +
622B MET* 1.3 56.8 + - + +
624B LEU* 3.4 7.2 + - + +
625B ALA* 2.9 30.3 + - + +
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Residues in contact with MET 622 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A SER* 3.5 24.7 - - - +
297A ILE* 4.5 19.3 - - + +
618B ARG* 2.9 40.3 + - + +
619B HIS* 3.7 24.7 - - + +
621B GLN* 1.3 77.5 - - + +
623B LYS* 1.3 58.2 + - + +
625B ALA* 3.3 6.5 + - - +
626B ARG* 2.9 38.4 + - - +
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Residues in contact with LYS 623 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B ASN 5.4 7.9 - - - +
96B THR* 6.1 0.9 - - - +
270B TYR* 3.4 47.4 + - + +
619B HIS* 2.9 45.9 + - - +
620B ILE* 3.3 6.2 + - - +
622B MET* 1.3 73.5 - - + +
624B LEU* 1.3 62.8 + - - +
626B ARG* 3.4 26.9 + - - +
627B LEU* 2.9 28.8 + - - +
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Residues in contact with LEU 624 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B TYR* 4.0 23.6 - - + -
275B LEU* 4.4 16.2 - - + +
276B LEU* 3.7 29.2 - - + -
616B LYS* 4.1 30.7 - - + +
620B ILE* 2.9 23.2 + - + +
621B GLN* 3.9 5.6 - - + +
623B LYS* 1.3 73.4 - - - +
625B ALA* 1.3 60.2 + - - +
627B LEU* 3.4 6.3 + - + +
628B GLU* 2.9 28.6 + - - +
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Residues in contact with ALA 625 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A PHE* 5.2 5.8 - - + -
297A ILE* 3.8 27.3 - - + +
621B GLN* 2.9 19.4 + - + +
622B MET* 3.7 5.6 - - - +
623B LYS 3.3 0.2 - - - -
624B LEU* 1.3 76.5 - - - +
626B ARG* 1.3 57.4 + - - +
628B GLU* 3.3 10.9 + - - +
629B PHE* 2.9 29.8 + - - +
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Residues in contact with ARG 626 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A SER* 3.4 33.7 + - - -
297A ILE* 3.7 20.7 + - + +
95B ASN 5.5 4.0 + - - -
96B THR* 5.4 14.3 + - + -
622B MET* 2.9 29.9 + - - +
623B LYS* 3.7 27.3 - - - +
624B LEU 3.3 0.2 - - - -
625B ALA* 1.3 77.3 - - - +
627B LEU* 1.3 57.9 + - - +
629B PHE* 3.3 2.7 + - - +
630B GLU* 3.0 49.9 + - + +
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Residues in contact with LEU 627 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B THR* 3.7 23.8 - - + -
97B MET 3.4 22.9 - - - +
98B ARG* 3.4 33.5 + - + +
270B TYR* 5.6 2.7 - - + +
276B LEU* 3.7 32.5 - - + -
623B LYS 2.9 18.1 + - - +
624B LEU* 3.7 7.4 - - + +
626B ARG* 1.3 76.1 - - - +
628B GLU* 1.3 60.8 - - - +
630B GLU* 3.9 2.2 + - - +
631B SER* 3.6 18.7 + - - -
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Residues in contact with GLU 628 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A ARG* 3.8 18.7 - - - +
281A PHE* 4.1 18.4 + - - +
624B LEU 2.9 16.5 + - - +
625B ALA* 3.5 12.2 - - - +
627B LEU* 1.3 76.6 - - - +
629B PHE* 1.3 75.6 + - - +
631B SER* 3.3 6.6 + - - -
632B LEU* 3.0 39.7 + - - +
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Residues in contact with PHE 629 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A PHE* 4.7 15.5 - + + -
297A ILE* 4.4 4.5 - - + -
298A THR* 3.3 57.9 - - + -
300A LYS* 3.8 20.2 - - - -
625B ALA 2.9 17.4 + - - +
626B ARG* 3.3 5.6 + - - +
628B GLU* 1.3 80.5 + - - +
630B GLU* 1.3 75.4 + - - +
632B LEU* 3.3 24.1 + - + +
633B GLU* 2.9 48.9 + - + +
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Residues in contact with GLU 630 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A ILE 4.8 0.9 - - - +
298A THR 4.6 4.9 - - - +
98B ARG* 3.7 33.0 - - - +
626B ARG* 3.0 36.2 + - + +
627B LEU* 4.2 4.9 - - + +
628B GLU 3.3 0.2 - - - -
629B PHE* 1.3 93.7 - - - +
631B SER* 1.3 56.8 + - - +
633B GLU* 3.4 21.2 + - - +
634B ALA* 2.9 26.7 + - - +
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Residues in contact with SER 631 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B ARG* 5.8 0.4 - - - +
627B LEU 3.6 11.6 + - - -
628B GLU* 3.3 9.5 + - - -
629B PHE 3.3 0.4 - - - -
630B GLU* 1.3 74.8 - - - +
632B LEU* 1.3 61.6 + - - +
634B ALA* 3.3 8.7 + - - +
635B LEU* 2.9 27.4 + - - +
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Residues in contact with LEU 632 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A ARG 4.8 4.3 - - - +
280A LYS* 5.1 3.1 - - - -
281A PHE* 4.5 22.7 - - + +
628B GLU* 3.0 35.6 + - - +
629B PHE* 3.7 27.8 - - + +
631B SER* 1.3 77.0 - - - +
633B GLU* 1.3 60.1 + - + +
635B LEU* 3.3 15.4 + - + +
636B LYS* 2.9 29.7 + - + +
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Residues in contact with GLU 633 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629B PHE* 2.9 38.1 + - + +
630B GLU* 3.4 23.3 - - - +
632B LEU* 1.3 77.1 - - - +
634B ALA* 1.3 60.1 + - - +
636B LYS* 3.3 6.3 + - + +
637B GLN* 2.9 54.5 + - + +
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Residues in contact with ALA 634 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
630B GLU 2.9 15.3 + - - +
631B SER* 3.3 11.9 + - - +
633B GLU* 1.3 77.5 - - - +
635B LEU* 1.3 56.8 + - - +
637B GLN* 3.4 6.2 + - - +
638B GLN* 2.9 29.8 + - - +
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Residues in contact with LEU 635 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A LYS* 5.0 16.2 - - + -
631B SER 2.9 13.4 + - - +
632B LEU* 3.6 15.9 - - + +
634B ALA* 1.3 77.3 - - - +
636B LYS* 1.3 56.8 + - - +
638B GLN* 3.3 15.2 + - + +
639B GLN* 2.9 30.6 + - + +
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Residues in contact with LYS 636 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632B LEU* 2.9 20.5 + - + +
633B GLU* 3.7 9.4 - - + +
634B ALA 3.3 0.2 - - - -
635B LEU* 1.3 77.9 - - - +
637B GLN* 1.3 65.1 + - - +
639B GLN* 3.3 14.2 + - - +
640B MET* 2.9 29.5 + - + +
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Residues in contact with GLN 637 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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633B GLU* 2.9 42.2 + - + +
634B ALA* 3.9 5.6 - - - +
636B LYS* 1.3 77.7 - - - +
638B GLN* 1.3 64.8 + - - +
640B MET* 4.1 13.7 - - - +
641B LYS* 3.4 50.9 + - - +
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Residues in contact with GLN 638 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A ARG* 4.4 22.6 + - - +
634B ALA 2.9 18.4 + - - +
635B LEU* 3.6 15.5 - - + +
636B LYS 3.3 0.2 - - - -
637B GLN* 1.3 78.1 - - - +
639B GLN* 1.3 60.6 + - - +
641B LYS* 3.8 16.4 + - - +
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Residues in contact with GLN 639 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A LYS* 4.8 11.1 + - - +
81A LEU* 4.5 7.7 + - - +
84A GLU* 3.8 32.9 + - + +
85A ALA* 3.6 31.8 - - - +
635B LEU* 2.9 21.9 + - + +
636B LYS* 3.3 13.5 + - - +
638B GLN* 1.3 79.1 - - - +
640B MET* 1.3 84.3 + - - +
641B LYS 3.5 3.6 + - - -
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Residues in contact with MET 640 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A LYS* 4.4 37.9 - - + +
44A LYS* 5.5 4.9 - - + -
636B LYS* 2.9 15.7 + - + +
637B GLN* 4.1 18.4 - - - +
638B GLN 3.3 0.4 - - - -
639B GLN* 1.3 93.4 + - - +
641B LYS* 1.3 64.6 + - + +
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Residues in contact with LYS 641 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637B GLN* 3.4 37.5 + - - +
638B GLN* 3.8 11.6 + - - +
639B GLN 3.4 5.9 - - - -
640B MET* 1.3 83.5 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il