Contacts of the strand formed by residues 72 - 77 (chain A) in PDB entry 4HXG
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 LYS 72 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A ILE* 3.7 4.2 - - - +
67A SER* 2.6 47.1 + - - +
69A ASP* 4.6 4.5 - - - +
70A GLY 3.3 2.2 + - - -
71A LYS* 1.3 86.2 - - + +
73A ILE* 1.3 57.8 + - - +
89A VAL* 4.2 17.9 - - + +
90A ALA 3.1 15.3 - - - +
91A ASP* 4.0 5.8 - - + -
92A LEU* 3.9 8.1 - - - +
111A TRP* 4.4 6.5 - - + -
115A SER* 3.0 34.9 + - - -
116A ARG* 4.6 1.6 - - - +
159A THR* 3.9 16.2 + - - -
160A GLU* 5.0 11.7 + - - +
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Residues in contact with ILE 73 (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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28A ALA* 4.5 5.4 - - + -
45A ILE* 4.4 1.6 - - + -
47A ILE* 4.0 30.7 - - + -
58A ILE* 3.9 19.1 - - + -
64A PRO* 4.1 20.4 - - + -
65A ARG 3.4 15.7 - - - +
66A ILE* 4.5 6.3 - - + +
72A LYS* 1.3 74.9 - - - +
74A ALA* 1.3 69.6 + - - +
75A PHE* 4.1 1.9 + - - -
89A VAL* 3.5 1.5 - - - -
90A ALA* 2.7 60.8 + - + +
92A LEU* 4.1 21.1 - - + -
95A LEU* 4.4 2.7 - - + -
111A TRP* 4.6 2.5 - - - -
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Residues in contact with ALA 74 (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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63A MET 3.5 2.4 - - - +
64A PRO* 3.6 1.0 - - - +
65A ARG* 2.7 41.2 + - + +
73A ILE* 1.3 73.9 - - - +
75A PHE* 1.3 61.9 + - - +
87A ILE* 5.1 0.2 - - + -
88A TRP 3.2 12.3 - - - +
89A VAL* 4.3 6.1 - - + +
109A ILE* 4.2 18.2 - - + -
111A TRP* 3.7 25.9 - - + +
118A LEU* 4.5 9.6 - - + -
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Residues in contact with PHE 75 (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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45A ILE* 3.6 24.2 - - + -
58A ILE* 3.7 38.6 - - + -
61A ALA* 3.6 15.5 - - + -
62A SER 3.7 0.7 - - - +
63A MET 3.7 7.0 - - - -
64A PRO* 4.6 0.2 - - + -
73A ILE* 4.1 7.4 - - + -
74A ALA* 1.3 78.3 - - - +
76A MET* 1.3 69.8 + - - +
77A ARG* 3.7 28.5 - - + -
87A ILE* 3.6 6.4 - - - +
88A TRP* 2.8 68.6 + + + +
90A ALA* 3.9 19.7 - - + -
97A ALA* 4.3 7.6 - - + -
109A ILE* 4.8 1.8 - - - +
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Residues in contact with MET 76 (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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61A ALA* 3.1 11.6 - - - +
62A SER 2.9 34.2 + - - +
63A MET* 3.7 42.2 - - + -
75A PHE* 1.3 80.4 - - - +
77A ARG* 1.3 60.0 - - - +
78A PHE* 3.6 31.2 - - + -
85A ALA* 4.6 9.6 - - + -
86A GLN 3.6 9.0 - - - +
87A ILE* 4.1 16.8 - - + -
106A ILE* 3.6 40.6 - - + +
109A ILE* 4.0 13.5 - - + -
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Residues in contact with ARG 77 (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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58A ILE* 3.9 15.8 - - - +
59A GLU* 3.3 28.3 + - - +
60A ASP* 2.9 24.9 + - - +
61A ALA* 4.0 2.7 - - + +
75A PHE* 3.7 14.5 - - + -
76A MET* 1.3 76.9 - - - +
78A PHE* 1.3 66.1 + - - +
84A THR 3.9 0.5 - - - +
85A ALA* 3.3 1.4 - - - -
86A GLN* 2.9 52.7 + - + +
88A TRP* 3.4 44.5 - - - +
97A ALA* 5.9 0.2 - - - +
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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