Contacts of the helix formed by residues 631 - 645 (chain W) in PDB entry 5IY6
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 ARG 631 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299W ARG 4.0 1.8 + - - -
300W GLU* 2.9 30.5 + - - +
301W THR* 3.7 28.0 - - + +
302W ASP* 6.2 1.3 - - - +
417W ILE* 4.1 13.9 - - + -
419W GLU* 2.7 34.6 + - - -
420W PRO* 3.5 29.7 - - - +
629W GLN* 2.8 47.1 + - + +
630W SER* 1.3 80.2 - - - +
632W ILE* 1.4 69.2 + - + +
633W LEU 3.3 1.8 - - - +
634W LYS* 3.1 12.5 + - - +
635W ALA* 3.1 12.5 + - - +
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Residues in contact with ILE 632 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303W ALA 5.5 2.2 - - - +
415W THR* 4.2 17.9 - - + +
416W ILE 5.6 0.2 - - - +
417W ILE* 3.9 33.4 - - + -
436W SER* 3.9 32.5 - - - +
437W CYS 4.5 2.7 - - - +
438W MET* 3.8 34.8 - - + +
631W ARG* 1.4 77.7 - - + +
633W LEU* 1.4 61.3 + - + +
635W ALA* 3.0 11.5 + - + +
636W ARG* 2.9 26.2 + - - +
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Residues in contact with LEU 633 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244W ILE* 5.4 12.3 - - + -
438W MET 6.1 0.4 - - - +
627W TYR 5.0 4.0 - - - +
628W THR* 3.9 18.8 - - + +
629W GLN* 3.6 38.4 - - + +
631W ARG* 3.3 1.0 - - - +
632W ILE* 1.4 80.6 - - + +
634W LYS* 1.3 55.2 + - - +
636W ARG* 3.0 15.9 + - + +
637W LEU* 2.9 27.4 + - - +
651W PHE* 4.2 13.2 - - + -
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Residues in contact with LYS 634 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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628W THR* 4.0 14.5 - - + +
629W GLN 3.2 12.6 + - - +
630W SER* 4.0 13.2 - - - +
631W ARG 3.1 15.1 + - - +
633W LEU* 1.3 76.0 - - - +
635W ALA* 1.3 61.2 + - - +
637W LEU* 3.2 31.0 + - + +
638W GLU* 3.1 23.8 + - - +
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Residues in contact with ALA 635 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438W MET* 3.5 30.5 - - + +
631W ARG 3.1 10.1 + - - +
632W ILE* 3.0 18.1 + - + +
634W LYS* 1.3 75.9 - - - +
636W ARG* 1.4 60.6 + - - +
638W GLU* 3.4 9.2 + - - +
639W TYR* 3.1 18.0 + - - +
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Residues in contact with ARG 636 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240W ASP* 2.7 43.3 + - - -
244W ILE* 3.8 19.3 - - - +
438W MET* 3.2 32.8 + - + +
439W ASP* 2.9 30.3 + - + +
440W ALA* 3.2 15.8 - - - +
632W ILE 2.9 11.8 + - - +
633W LEU* 3.0 23.5 + - + +
635W ALA* 1.4 77.2 - - - +
637W LEU* 1.4 59.9 + - - +
639W TYR* 3.1 7.4 + - + +
640W LEU* 3.1 35.5 + - + +
651W PHE* 3.8 30.1 - - + -
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Residues in contact with LEU 637 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628W THR* 4.3 9.9 - - + -
633W LEU 2.9 15.4 + - - +
634W LYS* 3.2 38.3 + - + +
636W ARG* 1.4 68.4 - - - +
638W GLU* 1.3 59.5 + - - +
640W LEU* 3.4 5.2 + - - +
641W ARG* 2.9 31.5 + - + +
647W ARG* 3.7 34.3 - - + +
648W GLU* 4.6 16.2 - - + +
651W PHE* 4.0 27.3 - - + -
652W LEU* 5.1 5.6 - - + -
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Residues in contact with GLU 638 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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634W LYS* 3.1 9.2 + - - +
635W ALA* 3.5 12.6 - - - +
637W LEU* 1.3 81.3 - - - +
639W TYR* 1.3 62.0 + - - +
641W ARG* 2.8 46.2 + - - +
642W ASP* 3.1 21.3 + - + +
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Residues in contact with TYR 639 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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438W MET* 4.8 8.7 - - - -
439W ASP* 3.7 29.6 + - + -
441W SER* 4.5 10.0 + - - -
635W ALA 3.1 13.6 + - - +
636W ARG* 3.1 11.6 + - + +
638W GLU* 1.3 75.3 - - - +
640W LEU* 1.3 84.2 + - + +
642W ASP* 3.2 11.9 + - - +
643W GLN* 3.1 52.4 + - + +
644W PHE* 5.7 2.6 - + - -
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Residues in contact with LEU 640 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439W ASP* 4.5 5.4 - - - +
636W ARG* 3.1 22.3 + - + +
637W LEU* 4.0 3.4 - - - +
639W TYR* 1.3 97.6 - - + +
641W ARG* 1.3 56.9 + - - +
643W GLN* 4.5 3.4 - - - +
644W PHE* 2.8 68.2 + - + +
645W GLN 3.5 0.5 + - - -
647W ARG* 3.6 14.4 - - + +
651W PHE* 3.3 46.9 - - + -
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Residues in contact with ARG 641 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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637W LEU* 2.9 17.9 + - + +
638W GLU* 2.8 41.0 + - - +
640W LEU* 1.3 73.1 - - - +
642W ASP* 1.3 66.8 + - - +
645W GLN* 3.1 31.5 + - + +
647W ARG* 3.8 45.4 - - - +
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Residues in contact with ASP 642 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638W GLU* 3.1 13.0 + - + +
639W TYR* 3.2 16.4 + - - +
641W ARG* 1.3 80.7 - - - +
643W GLN* 1.4 88.4 + - - +
645W GLN* 4.8 6.6 + - - +
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Residues in contact with GLN 643 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639W TYR* 3.1 44.6 + - + +
640W LEU* 4.3 2.9 - - - +
642W ASP* 1.4 101.6 + - - +
644W PHE* 1.4 81.7 - - + +
645W GLN* 5.1 3.5 + - - +
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Residues in contact with PHE 644 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469W LYS* 3.4 59.2 - - + -
470W ILE* 5.8 0.4 - - - -
639W TYR* 5.7 3.1 - + - -
640W LEU* 2.8 53.3 + - + +
643W GLN* 1.4 87.7 - - + +
645W GLN* 1.3 63.4 + - - +
646W ILE* 3.0 30.1 + - + +
647W ARG* 4.4 11.4 - - - +
650W ASP* 5.0 6.3 - - + -
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Residues in contact with GLN 645 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640W LEU 3.5 1.6 + - - -
641W ARG* 3.1 24.2 + - + +
642W ASP 4.8 7.3 + - - +
643W GLN 5.1 2.8 + - - +
644W PHE* 1.3 77.5 - - - +
646W ILE* 1.4 51.3 + - + +
647W ARG* 2.8 44.3 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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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