Contacts of the helix formed by residues 632 - 642 (chain N) in PDB entry 5GJQ
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 GLN 632 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53K PHE* 4.1 33.9 - - + -
629N THR* 4.7 4.1 + - - -
631N GLU* 1.3 79.2 - - + +
633N CYS* 1.3 51.2 + - - +
634N PRO 3.2 1.8 - - - -
635N SER* 2.6 31.1 + - - +
636N VAL* 2.2 55.8 + - + +
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Residues in contact with CYS 633 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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623N GLY* 5.5 4.0 - - - -
626N LEU* 5.5 10.8 - - + -
629N THR 4.4 5.4 + - - +
630N PRO* 3.0 25.9 + - + +
632N GLN* 1.3 75.7 - - - +
634N PRO* 1.3 53.8 - - + +
636N VAL* 3.1 12.5 - - - +
637N VAL* 2.5 41.5 + - - +
655N ALA* 4.4 5.8 - - - -
656N LEU* 3.4 42.8 - - + -
659N CYS* 4.4 4.9 - - + -
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Residues in contact with PRO 634 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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630N PRO 3.0 16.8 - - - +
631N GLU 3.1 11.4 - - - +
632N GLN 3.4 0.4 - - - -
633N CYS* 1.3 87.7 - - + +
635N SER* 1.3 51.3 + - - +
637N VAL* 3.1 10.8 + - + +
638N SER* 2.5 40.2 + - - -
656N LEU* 3.5 6.3 - - + -
660N CYS* 5.3 0.4 - - - -
665N ASN* 5.2 3.4 - - + -
667N GLU* 5.1 6.3 - - + -
668N ALA* 3.3 43.3 - - + +
671N LEU* 5.1 6.6 - - + +
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Residues in contact with SER 635 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43J ARG* 5.3 8.8 + - - -
631N GLU 4.7 0.8 + - - -
632N GLN* 2.6 33.8 + - - +
634N PRO* 1.3 75.3 - - - +
636N VAL* 1.3 62.2 + - - +
638N SER* 3.3 18.6 - - - -
639N LEU* 4.0 5.7 + - - +
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Residues in contact with VAL 636 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53K PHE* 5.1 7.9 - - + -
57K GLN* 5.5 12.3 - - - +
626N LEU* 4.9 19.3 - - + -
632N GLN* 2.2 51.2 + - + +
633N CYS* 3.1 15.9 - - - +
635N SER* 1.3 72.9 - - - +
637N VAL* 1.3 64.5 + - + +
638N SER 3.0 0.2 + - - -
639N LEU* 3.2 20.6 + - - +
640N LEU* 5.0 2.5 - - - +
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Residues in contact with VAL 637 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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619N VAL* 5.1 8.3 - - + -
622N LEU* 6.3 1.8 - - + -
633N CYS* 2.5 39.3 + - - +
634N PRO* 3.2 15.3 - - + +
636N VAL* 1.3 75.0 - - + +
638N SER* 1.3 51.0 + - - +
639N LEU 2.9 1.3 - - - -
640N LEU* 2.5 17.1 + - + +
641N SER* 2.2 41.6 + - - +
652N ALA* 4.3 31.2 - - + +
655N ALA* 5.5 2.9 - - + -
656N LEU* 3.7 18.2 - - + +
671N LEU* 4.6 10.1 - - + -
672N LEU* 5.5 2.0 - - + -
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Residues in contact with SER 638 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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634N PRO 2.5 26.9 + - - -
635N SER* 3.3 17.5 - - - -
636N VAL 3.0 0.8 + - - -
637N VAL* 1.3 71.7 - - - +
639N LEU* 1.3 58.9 + - - +
641N SER* 2.5 23.1 + - - -
642N GLU* 3.9 6.1 + - - +
671N LEU* 5.0 6.1 - - - +
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Residues in contact with LEU 639 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43J ARG* 4.3 14.6 - - + +
47J ALA* 4.2 26.0 - - + -
50J ASN* 5.2 7.6 - - - +
57K GLN* 4.0 21.8 - - + -
60K TYR* 5.0 8.3 - - + -
61K ILE* 3.4 33.2 - - + -
635N SER 4.8 3.8 - - - +
636N VAL* 3.2 12.6 + - - +
637N VAL 2.8 1.7 + - - -
638N SER* 1.3 77.3 - - - +
640N LEU* 1.3 60.7 + - + +
642N GLU* 2.7 39.8 + - - +
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Residues in contact with LEU 640 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60K TYR* 2.9 40.6 - - + +
64K GLU* 4.3 6.7 - - - +
603N LEU* 5.3 4.9 - - + -
606N ALA* 6.0 1.3 - - + -
619N VAL* 3.6 36.3 - - + -
622N LEU* 4.8 10.3 - - + -
636N VAL 5.0 1.8 - - - +
637N VAL* 2.5 22.0 + - + +
639N LEU* 1.3 73.4 - - + +
641N SER* 1.3 65.6 + - - +
642N GLU* 3.1 2.4 + - - -
643N SER* 3.6 14.9 + - - -
648N VAL* 3.6 24.5 - - + +
649N ARG* 3.7 10.6 - - - +
652N ALA* 4.5 8.5 - - + -
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Residues in contact with SER 641 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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637N VAL* 2.2 30.2 + - - +
638N SER* 2.5 36.5 + - - -
640N LEU* 1.3 69.0 - - - +
642N GLU* 1.3 61.8 + - - +
649N ARG* 3.4 22.0 + - - +
652N ALA* 4.7 9.2 - - - -
671N LEU* 3.8 24.0 - - - +
672N LEU* 6.3 0.7 - - - -
675N MET* 4.4 16.4 - - - +
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Residues in contact with GLU 642 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50J ASN* 5.7 2.1 + - - -
51J GLU* 2.8 52.3 - - + +
54J ALA* 5.1 2.3 - - + +
64K GLU* 4.9 3.3 - - - +
638N SER 4.2 4.5 - - - +
639N LEU* 2.7 24.5 + - - +
641N SER* 1.3 78.3 + - - +
643N SER* 1.3 61.0 + - - +
649N ARG* 4.1 11.7 - - - +
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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