Contacts of the helix formed by residues 617 - 641 (chain A) in PDB entry 6R7Z
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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A ARG* 5.3 13.7 - - + +
266A ALA* 4.4 12.3 - - + -
267A ASN* 6.1 1.6 - - + +
614A PRO* 5.7 2.9 - - + -
615A ASP 4.4 2.7 - - - +
616A LYS* 1.3 92.5 - - + +
618A ARG* 1.3 66.2 + - - +
619A HIS* 3.5 28.5 - - + +
620A ILE* 3.7 14.8 - - + -
621A GLN* 3.1 21.2 + - - +
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Residues in contact with ARG 618 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617A PRO* 1.3 76.0 - - - +
619A HIS* 1.3 55.6 + - - +
621A GLN* 3.1 6.5 + - - +
622A MET* 2.7 35.0 + - - +
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Residues in contact with HIS 619 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617A PRO* 3.7 27.9 - - + +
618A ARG* 1.3 77.6 + - - +
620A ILE* 1.3 75.6 + - + +
622A MET* 3.6 9.2 - - - +
623A LYS* 2.9 28.9 + - - +
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Residues in contact with ILE 620 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A ALA* 5.6 5.4 - - + +
270A TYR* 5.5 11.9 - - + -
616A LYS* 4.6 5.8 - - + -
617A PRO* 3.7 29.1 + - + -
618A ARG 3.3 0.6 - - - -
619A HIS* 1.3 91.6 + - + +
621A GLN* 1.3 55.7 + - - +
623A LYS* 3.3 6.2 + - - +
624A LEU* 2.9 28.2 + - - +
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Residues in contact with GLN 621 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616A LYS* 4.7 10.3 - - + +
617A PRO 3.1 19.4 + - - +
618A ARG* 3.1 7.7 + - - +
620A ILE* 1.3 75.4 - - - +
622A MET* 1.3 52.5 + - - +
624A LEU* 3.3 6.8 + - - +
625A ALA* 2.7 35.3 + - - +
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Residues in contact with MET 622 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618A ARG 2.7 19.3 + - - +
619A HIS* 3.6 10.5 - - - +
620A ILE 3.3 0.2 - - - -
621A GLN* 1.3 74.3 - - - +
623A LYS* 1.3 56.3 + - - +
625A ALA* 3.6 7.5 - - - +
626A ARG* 2.8 30.0 + - - +
296B SER* 6.1 3.6 - - - +
297B ILE* 5.2 14.6 - - + -
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Residues in contact with LYS 623 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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619A HIS 2.9 17.9 + - - +
620A ILE* 3.7 7.2 - - - +
622A MET* 1.3 75.6 - - - +
624A LEU* 1.3 58.7 + - - +
626A ARG* 3.4 7.0 + - - +
627A LEU* 2.9 27.2 + - - +
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Residues in contact with LEU 624 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620A ILE 2.9 17.4 + - - +
621A GLN* 3.7 7.2 - - - +
623A LYS* 1.3 77.0 - - - +
625A ALA* 1.3 57.0 + - - +
627A LEU* 3.4 7.8 + - - +
628A GLU* 2.8 28.1 + - - +
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Residues in contact with ALA 625 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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621A GLN 2.7 22.1 + - - +
622A MET* 3.6 9.2 - - - +
624A LEU* 1.3 72.3 - - - +
626A ARG* 1.3 53.9 + - - +
628A GLU* 3.2 7.6 + - - +
629A PHE* 2.6 37.5 + - - +
297B ILE* 5.0 13.2 - - + -
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Residues in contact with ARG 626 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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622A MET 2.8 21.6 + - - +
623A LYS* 3.6 7.9 - - - +
624A LEU 3.3 0.2 - - - -
625A ALA* 1.3 72.8 - - - +
627A LEU* 1.3 57.6 + - - +
629A PHE* 3.7 7.3 - - - +
630A GLU* 2.8 31.4 + - - +
296B SER 5.8 0.9 - - - +
297B ILE* 4.2 17.2 + - - +
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Residues in contact with LEU 627 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A MET 5.6 5.8 - - - +
623A LYS 2.9 17.6 + - - +
624A LEU* 3.7 8.1 - - - +
625A ALA 3.3 0.2 - - - -
626A ARG* 1.3 76.5 - - - +
628A GLU* 1.3 60.9 + - - +
630A GLU* 3.9 6.3 - - - +
631A SER* 3.3 20.4 + - - -
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Residues in contact with GLU 628 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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624A LEU 2.8 17.2 + - - +
625A ALA* 3.5 9.2 - - - +
626A ARG 3.2 0.2 - - - -
627A LEU* 1.3 76.2 - - - +
629A PHE* 1.3 58.8 + - - +
631A SER* 3.2 7.5 + - - -
632A LEU* 2.9 27.3 + - - +
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Residues in contact with PHE 629 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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625A ALA 2.6 21.0 + - - +
626A ARG* 3.8 7.6 - - - +
628A GLU* 1.3 71.1 - - - +
630A GLU* 1.3 63.3 + - - +
632A LEU* 3.3 10.6 + - + +
633A GLU* 2.8 38.5 + - + +
281B PHE* 5.5 12.3 - - + -
297B ILE 4.6 4.0 - - - +
298B THR* 3.2 48.9 - - - -
300B LYS* 6.2 1.3 - - + -
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Residues in contact with GLU 630 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626A ARG 2.8 18.1 + - - +
627A LEU* 3.9 7.4 - - - +
629A PHE* 1.3 80.1 - - - +
631A SER* 1.3 57.4 + - - +
633A GLU* 3.4 6.6 + - - +
634A ALA* 2.8 28.3 + - - +
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Residues in contact with SER 631 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
627A LEU 3.3 12.4 + - - -
628A GLU* 3.2 11.3 + - - -
630A GLU* 1.3 75.0 - - - +
632A LEU* 1.3 60.5 + - - +
634A ALA* 3.3 8.5 + - - +
635A LEU* 2.8 27.7 + - - +
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Residues in contact with LEU 632 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628A GLU 2.9 13.8 + - - +
629A PHE* 3.3 18.1 + - + +
631A SER* 1.3 77.9 - - - +
633A GLU* 1.3 56.1 + - - +
635A LEU* 3.3 8.9 + - - +
636A LYS* 3.0 25.8 + - - +
281B PHE* 5.8 8.1 - - + -
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Residues in contact with GLU 633 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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629A PHE* 2.8 30.1 + - + +
630A GLU* 3.7 7.9 - - - +
632A LEU* 1.3 73.8 - - - +
634A ALA* 1.3 60.0 + - - +
636A LYS* 3.4 7.6 + - - +
637A GLN* 3.0 28.2 + - - +
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Residues in contact with ALA 634 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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630A GLU 2.8 17.4 + - - +
631A SER* 3.5 10.8 - - - +
632A LEU 3.3 0.2 - - - -
633A GLU* 1.3 75.7 - - - +
635A LEU* 1.3 57.8 + - - +
637A GLN* 3.4 6.1 + - - +
638A GLN* 2.9 30.1 + - - +
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Residues in contact with LEU 635 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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631A SER 2.8 16.5 + - - +
632A LEU* 3.3 9.4 + - - +
634A ALA* 1.3 74.6 - - - +
636A LYS* 1.3 58.4 + - - +
638A GLN* 3.3 7.1 + - - +
639A GLN* 2.8 30.4 + - - +
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Residues in contact with LYS 636 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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632A LEU 3.0 16.3 + - - +
633A GLU* 3.7 9.2 - - - +
634A ALA 3.3 0.4 - - - -
635A LEU* 1.3 75.5 - - - +
637A GLN* 1.3 57.7 + - - +
639A GLN* 3.3 7.4 + - - +
640A MET* 2.9 29.3 + - - +
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Residues in contact with GLN 637 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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633A GLU 3.0 16.3 + - - +
634A ALA* 3.8 6.5 - - - +
636A LYS* 1.3 76.7 - - - +
638A GLN* 1.3 62.0 + - - +
640A MET* 3.4 6.3 + - - +
641A LYS* 3.3 23.7 + - - +
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Residues in contact with GLN 638 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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634A ALA 2.9 17.6 + - - +
635A LEU* 3.7 7.9 - - - +
637A GLN* 1.3 75.9 - - - +
639A GLN* 1.3 62.5 + - - +
641A LYS* 4.0 13.0 + - - +
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Residues in contact with GLN 639 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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635A LEU 2.8 17.5 + - - +
636A LYS* 3.6 8.5 - - - +
637A GLN 3.2 0.2 - - - -
638A GLN* 1.3 78.1 - - - +
640A MET* 1.3 62.9 + - - +
641A LYS 3.3 8.1 - - - +
84B GLU 5.7 4.7 - - - +
85B ALA* 5.9 5.4 - - - -
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Residues in contact with MET 640 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636A LYS 2.9 16.6 + - - +
637A GLN* 3.4 7.8 + - - +
639A GLN* 1.3 78.6 - - - +
641A LYS* 1.3 60.8 + - - +
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Residues in contact with LYS 641 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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637A GLN 3.3 14.8 + - - +
638A GLN* 4.0 8.9 - - - +
639A GLN 3.3 11.7 - - - +
640A MET* 1.3 82.6 - - - +
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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