Contacts of the helix formed by residues 62 - 69 (chain D) in PDB entry 4XCS
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 62 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58D ALA* 3.2 19.6 + - - +
59D PHE 3.5 3.4 - - - +
61D ASP* 1.3 84.7 - - + +
63D ALA* 1.3 64.1 + - - +
64D GLU* 3.1 3.1 - - - -
65D GLU* 2.9 60.7 + - - +
66D PHE* 3.5 9.3 - - - -
153D VAL* 3.5 32.0 - - + +
154D ASP* 2.8 36.7 + - - -
157D LEU* 3.2 15.2 - - - +
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Residues in contact with ALA 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D PHE 3.0 10.9 + - - +
60D SER 3.2 16.4 + - - +
61D ASP 3.4 1.2 + - - -
62D ARG* 1.3 77.4 - - - +
64D GLU* 1.3 57.6 + - - +
65D GLU 3.3 0.2 - - - -
66D PHE* 3.3 12.9 + - - +
67D LYS* 2.9 24.7 + - - +
71D CYS 4.9 0.3 - - - +
73D VAL* 5.4 1.8 - - + -
101D ASN* 4.0 13.9 - - + +
102D ILE* 4.0 20.6 - - + -
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Residues in contact with GLU 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61D ASP 5.0 0.4 + - - -
62D ARG* 3.1 1.9 - - - -
63D ALA* 1.3 75.8 - - + +
65D GLU* 1.3 61.6 + - + +
66D PHE 3.0 1.8 - - - -
67D LYS* 3.0 15.2 + - + +
68D LYS* 2.7 65.1 + - - +
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Residues in contact with GLU 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D ARG* 2.9 63.9 + - + +
64D GLU* 1.3 78.9 - - + +
66D PHE* 1.3 61.7 + - - +
68D LYS* 3.4 20.1 - - - +
69D LEU* 3.5 13.3 + - - +
157D LEU* 3.7 20.8 - - + +
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Residues in contact with PHE 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D VAL* 4.0 18.2 - - + -
59D PHE* 3.9 30.3 - + - -
62D ARG 3.5 16.6 - - - -
63D ALA* 3.3 9.3 + - - +
64D GLU 3.0 0.4 - - - -
65D GLU* 1.3 76.9 - - - +
67D LYS* 1.3 55.0 + - - +
69D LEU* 2.9 13.7 + - + -
71D CYS* 2.8 58.4 + - + +
73D VAL* 3.5 23.6 - - + -
153D VAL* 3.8 19.1 - - + -
156D THR* 4.1 6.7 - - + -
157D LEU* 3.4 45.1 - - + -
160D VAL* 4.3 4.5 - - + -
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Residues in contact with LYS 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63D ALA 2.9 14.1 + - - +
64D GLU* 3.0 17.9 + - + +
66D PHE* 1.3 76.5 - - - +
68D LYS* 1.3 72.4 + - + +
70D ASN* 2.9 20.3 + - - -
71D CYS 3.6 8.4 + - - +
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Residues in contact with LYS 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64D GLU* 2.7 65.4 + - - +
65D GLU* 3.4 12.8 - - - +
67D LYS* 1.3 88.4 - - + +
69D LEU* 1.3 63.6 + - + +
70D ASN* 3.1 3.4 + - - +
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Residues in contact with LEU 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D GLU 3.5 8.5 - - - +
66D PHE* 2.9 11.3 + - + +
68D LYS* 1.3 80.1 - - + +
70D ASN* 1.3 65.4 + - - +
71D CYS* 3.2 6.0 + - + -
157D LEU* 3.7 34.1 - - + +
160D VAL* 4.2 12.1 - - + -
161D GLN* 3.9 41.3 - - + +
164D GLN* 2.8 36.6 + - - +
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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
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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