Contacts of the helix formed by residues 633 - 650 (chain B) in PDB entry 1RL3
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 LEU 633 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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535B LEU* 3.8 24.7 - - + +
536B PHE* 3.8 32.3 - - + -
539B LEU* 4.2 13.5 - - + -
547B ILE* 4.5 11.4 - - + -
572B PHE* 3.8 16.4 - - + -
624B ILE* 5.1 6.3 - - + -
629B TYR* 2.8 49.4 + - + +
632B ILE* 1.3 80.7 - - - +
634B MET* 1.3 64.2 + - - +
635B GLY 3.5 0.9 - - - -
636B SER* 3.2 9.4 + - - +
637B THR* 3.1 27.3 + - - +
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Residues in contact with MET 634 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604B ILE* 3.7 39.9 - - + +
629B TYR* 2.9 29.7 + - + +
630B ARG* 3.3 56.3 - - - +
632B ILE 3.9 0.4 - - - -
633B LEU* 1.3 74.7 - - - +
635B GLY* 1.3 69.1 + - - +
637B THR* 2.9 6.9 + - - -
638B LEU* 2.8 41.7 + - + +
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Residues in contact with GLY 635 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
630B ARG 5.1 1.6 + - - -
631B ARG 6.2 0.6 - - - -
632B ILE 5.2 2.0 + - - -
633B LEU 3.5 1.0 - - - +
634B MET* 1.3 81.8 - - - +
636B SER* 1.3 57.3 + - - +
638B LEU* 3.4 4.4 + - - +
639B ARG* 2.9 48.7 + - - +
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Residues in contact with SER 636 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535B LEU 4.3 11.3 + - - -
538B HIS* 3.7 38.8 + - - +
632B ILE 4.7 5.8 + - - -
633B LEU* 3.2 16.5 + - - +
634B MET 3.3 0.4 - - - -
635B GLY* 1.3 74.5 - - - +
637B THR* 1.3 58.3 + - - +
639B ARG* 3.4 16.5 - - - +
640B LYS* 2.7 39.2 + - - +
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Residues in contact with THR 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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535B LEU* 4.2 20.0 + - + +
600B GLU* 5.0 0.2 - - + -
604B ILE* 3.8 18.2 - - + -
629B TYR* 3.2 25.5 + - - +
633B LEU* 3.1 14.7 + - - +
634B MET 2.9 8.6 + - - -
636B SER* 1.3 80.6 + - - +
638B LEU* 1.3 65.5 + - - +
640B LYS* 3.9 4.2 - - - +
641B ARG* 3.0 51.5 + - - +
667B ASP* 4.7 6.0 - - - +
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Residues in contact with LEU 638 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604B ILE* 3.7 27.4 - - + -
605B TYR* 3.2 30.3 - - + +
634B MET* 2.8 42.5 + - + +
635B GLY* 4.0 4.3 - - - +
637B THR* 1.3 69.3 - - - +
639B ARG* 1.3 69.0 + - - +
641B ARG* 3.0 12.5 + - - +
642B LYS* 2.8 27.2 + - - +
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Residues in contact with ARG 639 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538B HIS* 6.3 0.9 - - - -
635B GLY* 2.9 28.3 + - - +
636B SER* 3.4 23.1 - - - +
638B LEU* 1.3 78.9 - - - +
640B LYS* 1.3 66.4 + - - +
641B ARG 2.8 1.7 + - - -
642B LYS* 3.2 4.4 + - - +
643B MET* 3.1 25.8 + - + +
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Residues in contact with LYS 640 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534B VAL* 3.3 11.5 - - - +
535B LEU* 6.5 0.4 - - + -
538B HIS* 4.3 24.2 + - + -
636B SER 2.7 21.7 + - - +
637B THR* 3.9 4.7 - - - +
639B ARG* 1.3 73.5 - - - +
641B ARG* 1.3 59.5 + - - +
643B MET* 3.8 7.1 - - - +
644B TYR* 3.1 59.9 + - + +
666B ALA* 3.3 20.5 + - - +
667B ASP* 3.3 24.8 + - - +
669B LEU* 2.7 31.4 + - - -
671B PRO* 4.7 7.4 - - + +
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Residues in contact with ARG 641 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600B GLU* 3.2 37.8 + - - +
601B LEU* 3.9 14.1 - - - +
604B ILE* 4.5 4.9 - - - +
605B TYR* 4.9 7.6 + - - -
637B THR* 3.0 36.2 + - - +
638B LEU* 3.0 14.6 + - + +
639B ARG 2.8 1.4 + - - -
640B LYS* 1.3 73.4 - - - +
642B LYS* 1.3 55.2 + - - +
643B MET 2.8 14.7 + - - -
644B TYR 2.9 12.1 + - - -
645B GLU* 2.9 19.3 + - - +
660B TRP* 4.6 4.2 - - - +
663B LEU* 3.7 47.6 - - + +
664B THR 5.4 0.2 - - - +
666B ALA* 4.6 9.7 - - + +
667B ASP* 3.3 38.4 + - - +
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Residues in contact with LYS 642 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638B LEU* 2.8 18.9 + - + +
639B ARG* 4.0 4.3 - - - +
641B ARG* 1.3 72.2 - - - +
643B MET* 1.3 58.2 - - - +
645B GLU* 3.4 39.7 - - - +
646B GLU* 6.0 0.5 - - - +
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Residues in contact with MET 643 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639B ARG* 3.1 20.1 + - + +
640B LYS* 3.8 10.3 - - - +
641B ARG 2.8 2.8 - - - -
642B LYS* 1.3 80.4 - - - +
644B TYR* 1.3 97.0 + - + +
645B GLU 3.5 0.4 - - - -
646B GLU 5.5 0.3 + - - -
647B PHE* 5.1 4.9 + - - +
694B LEU* 6.5 0.2 - - + -
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Residues in contact with TYR 644 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640B LYS* 3.1 54.3 - - + +
641B ARG 2.9 4.1 + - - +
643B MET* 1.3 107.9 - - + +
645B GLU* 1.3 68.1 + - - +
646B GLU 3.5 1.3 - - - -
647B PHE* 3.9 21.7 - + + -
648B LEU* 3.0 38.9 + - + +
666B ALA* 4.3 7.6 - - + -
669B LEU* 3.9 15.7 - - + -
671B PRO* 3.7 16.7 - - + +
694B LEU* 3.9 17.5 - - + +
746B VAL* 3.2 35.2 - - + +
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Residues in contact with GLU 645 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641B ARG* 2.9 13.4 + - - +
642B LYS* 3.4 47.7 + - - +
643B MET 3.5 1.4 - - - -
644B TYR* 1.3 78.4 - - - +
646B GLU* 1.3 70.1 + - + +
648B LEU* 3.6 4.2 - - - +
649B SER* 3.0 26.8 + - - -
659B LYS* 5.8 8.3 - - - -
662B ARG* 4.3 7.8 - - - -
663B LEU* 5.5 10.1 - - + +
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Residues in contact with GLU 646 (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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642B LYS 6.0 0.4 - - - +
643B MET 5.5 0.4 + - - -
645B GLU* 1.3 84.9 - - + +
647B PHE* 1.3 68.6 + - - +
648B LEU 2.8 3.1 + - - -
649B SER* 2.8 30.0 + - - -
650B LYS* 2.9 35.5 + - - +
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Residues in contact with PHE 647 (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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643B MET 5.1 3.1 + - - +
644B TYR* 3.6 20.3 + + + +
645B GLU 3.5 0.2 - - - -
646B GLU* 1.3 77.8 - - - +
648B LEU* 1.3 76.1 + - + +
650B LYS* 4.0 6.5 + - - +
651B VAL* 3.6 18.2 + - + +
692B ILE* 3.4 26.5 - - + -
693B ILE 2.9 29.6 - - - -
694B LEU* 3.7 30.1 - - + -
718B PRO* 5.0 0.9 - - + -
719B SER* 3.9 23.7 + - - -
746B VAL* 4.8 3.8 - - + -
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Residues in contact with LEU 648 (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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644B TYR* 3.0 29.0 + - + +
645B GLU* 3.6 3.4 - - - +
646B GLU 2.8 1.4 + - - -
647B PHE* 1.3 95.2 - - + +
649B SER* 1.3 63.6 + - - +
650B LYS 3.2 2.0 - - - -
651B VAL* 3.1 17.2 + - + +
654B LEU* 3.3 34.6 - - + +
655B GLU 5.5 0.2 + - - -
662B ARG* 3.8 39.7 + - + +
665B VAL* 4.2 9.4 - - + -
666B ALA* 3.9 24.0 - - + +
669B LEU* 4.2 11.9 - - + -
692B ILE* 5.0 7.6 - - + -
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Residues in contact with SER 649 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645B GLU 3.0 11.3 + - - -
646B GLU* 2.8 37.8 + - - -
648B LEU* 1.3 77.6 - - - +
650B LYS* 1.3 62.1 + - - +
651B VAL 3.1 3.4 + - - -
652B SER* 4.4 4.5 + - - -
655B GLU* 5.7 6.1 + - - +
662B ARG* 4.0 16.5 - - - +
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Residues in contact with LYS 650 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646B GLU* 2.9 55.2 + - - +
647B PHE* 4.1 7.4 - - - +
649B SER* 1.3 79.6 - - - +
651B VAL* 1.3 56.4 + - - +
652B SER* 3.3 8.4 + - - -
719B SER* 4.1 11.1 + - - -
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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