Contacts of the helix formed by residues 94 - 103 (chain A) in PDB entry 4ZDV
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 PRO 94 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A ASP 4.1 11.2 - - - +
57A HIS* 4.6 7.6 - - - +
58A VAL 3.7 7.2 - - - +
59A ASN* 4.2 9.2 - - - +
92A SER 3.5 5.8 - - - +
93A THR* 1.3 95.7 - - + +
95A ILE* 1.3 65.6 + - - +
96A ALA* 4.3 4.3 - - + +
97A ASP* 3.1 28.1 + - - +
98A ILE* 3.4 8.1 + - - +
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Residues in contact with ILE 95 (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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31A ILE* 3.9 13.5 - - + -
33A VAL* 3.9 22.2 - - + -
54A VAL* 4.0 13.9 - - + -
55A PRO 3.6 22.4 - - - +
56A ASP* 3.7 8.2 + - - +
58A VAL* 2.8 23.4 + - + +
59A ASN 5.5 0.2 - - - -
60A MET* 3.7 20.2 - - - -
63A LEU* 3.8 29.6 - - + -
93A THR 3.6 0.6 + - - -
94A PRO* 1.3 73.4 - - - +
96A ALA* 1.3 57.7 + - - +
98A ILE* 4.3 0.4 - - - -
99A TYR* 2.8 29.6 + - - +
109A LEU* 4.0 16.8 - - + -
111A MET* 4.1 1.1 - - + -
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Residues in contact with ALA 96 (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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31A ILE* 4.3 8.3 - - + -
56A ASP* 3.1 42.9 + - + +
94A PRO* 4.8 4.3 - - + -
95A ILE* 1.3 78.3 - - - +
97A ASP* 1.3 66.7 + - - +
99A TYR* 3.5 4.9 - - - +
100A GLU* 3.3 25.0 + - - +
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Residues in contact with ASP 97 (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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93A THR* 3.8 12.4 - - + +
94A PRO* 3.1 33.1 + - - +
96A ALA* 1.3 80.7 - - - +
98A ILE* 1.3 66.0 + - - +
100A GLU* 3.3 20.6 + - - +
101A GLN* 3.2 39.5 + - - +
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Residues in contact with ILE 98 (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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60A MET* 3.6 39.0 - - + -
83A VAL* 4.3 10.1 - - + -
88A MET* 4.9 8.3 - - + -
91A VAL* 4.8 5.2 - - + -
93A THR* 3.8 21.8 - - + +
94A PRO 3.8 7.2 - - - +
95A ILE 3.3 6.8 + - - +
97A ASP* 1.3 76.4 - - - +
99A TYR* 1.3 53.7 + - - +
101A GLN* 3.1 17.1 + - - +
102A GLU* 2.7 49.7 + - + +
109A LEU* 4.1 17.7 - - + -
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Residues in contact with TYR 99 (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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20A VAL* 4.3 3.8 - - - +
24A ARG* 3.8 33.9 + - - +
31A ILE* 3.4 41.3 - - + -
32A PRO* 4.0 14.4 - - + +
95A ILE 2.8 18.0 + - - +
96A ALA 3.5 6.1 - - - +
98A ILE* 1.3 76.0 - - - +
100A GLU* 1.3 65.4 + - + +
103A LYS* 3.0 66.9 + - + +
107A GLY* 2.6 33.9 + - - -
109A LEU* 4.0 17.4 - - + +
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Residues in contact with GLU 100 (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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96A ALA 3.3 15.5 + - - +
97A ASP* 3.4 26.5 - - - +
99A TYR* 1.3 84.1 - - + +
101A GLN* 1.3 66.5 + - + +
103A LYS* 4.7 13.6 + - - +
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Residues in contact with GLN 101 (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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93A THR* 5.4 2.2 - - - +
97A ASP* 3.2 30.5 + - - +
98A ILE* 3.1 21.3 + - - +
100A GLU* 1.3 87.4 + - + +
102A GLU* 1.3 79.6 + - + +
103A LYS 3.8 0.2 - - - -
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Residues in contact with GLU 102 (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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83A VAL* 3.8 26.7 - - + +
84A ASN* 3.6 33.5 + - - +
98A ILE* 2.7 28.1 + - + +
101A GLN* 1.3 97.5 - - + +
103A LYS* 1.3 66.0 + - - +
104A ASP* 3.6 1.4 + - - -
109A LEU* 3.8 11.2 - - + +
110A TYR 5.4 1.0 + - - -
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Residues in contact with LYS 103 (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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99A TYR* 3.0 67.6 + - + +
100A GLU* 4.7 12.0 + - - +
101A GLN 3.8 0.4 - - - -
102A GLU* 1.3 80.7 - - - +
104A ASP* 1.3 69.0 + - - +
107A GLY* 4.4 10.1 - - - +
108A PHE 3.7 7.9 - - - +
109A LEU* 4.1 5.6 - - - +
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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