Contacts of the helix formed by residues 79 - 90 (chain A) in PDB entry 4Z2C
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 GLY 79 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A MET* 4.2 0.2 - - - -
78A HIS* 1.3 81.5 - - - +
80A ASP* 1.3 65.3 + - - -
81A SER* 3.1 4.9 - - - -
82A SER* 3.4 16.4 + - - -
83A ILE* 3.4 16.5 + - - +
119B ARG* 3.7 14.5 - - - +
15E T 3.6 15.2 + - - -
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Residues in contact with ASP 80 (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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65A ALA* 5.4 0.7 - - - +
68A THR* 2.9 36.2 + - - -
69A GLY* 5.1 1.6 + - - -
72A MET* 3.5 27.5 - - + +
79A GLY* 1.3 72.3 - - - -
81A SER* 1.3 56.2 + - - +
83A ILE* 3.3 6.2 + - - +
84A TYR* 2.9 28.1 + - - +
118A GLN* 3.5 15.1 - - - +
65B ALA* 4.5 4.5 - - - +
80B ASP* 4.8 8.2 - - - +
118B GLN* 4.3 15.7 + - - +
119B ARG* 5.1 0.4 - - - +
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Residues in contact with SER 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A GLY* 4.9 2.2 - - - -
80A ASP* 1.3 80.7 - - - +
82A SER* 1.3 56.9 + - - +
84A TYR* 4.1 5.5 - - - +
85A GLU* 2.9 32.8 + - - +
118A GLN* 4.7 4.0 - - - +
15E T 6.3 3.1 - - - -
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Residues in contact with SER 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A VAL* 4.7 0.2 - - - +
78A HIS* 5.2 0.9 - - - -
79A GLY* 3.4 16.3 + - - -
80A ASP 3.3 0.4 - - - -
81A SER* 1.3 78.4 - - - +
83A ILE* 1.3 60.3 + - - +
85A GLU* 3.6 5.0 - - - +
86A ALA* 2.9 30.1 + - - +
13E T 4.7 9.9 - - - +
14E A 3.6 39.2 + - - -
15E T 5.5 5.6 - - - +
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Residues in contact with ILE 83 (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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42A VAL* 4.3 7.4 - - + -
46A ILE* 3.3 30.3 - - + +
68A THR* 4.0 20.6 - - + +
71A VAL* 3.7 28.3 - - + -
72A MET* 3.7 30.5 - - + +
76A HIS* 3.5 32.3 - - + +
78A HIS 4.9 0.4 - - - +
79A GLY 3.6 12.6 - - - +
80A ASP* 3.3 7.1 + - - +
82A SER* 1.3 73.2 - - - +
84A TYR* 1.3 65.6 + - - +
86A ALA 3.1 2.1 + - - -
87A MET* 2.9 22.1 + - + +
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Residues in contact with TYR 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A SER* 3.6 18.8 - - - -
68A THR* 3.8 11.9 - - + +
80A ASP 2.9 10.7 + - - +
81A SER* 4.1 3.1 - - - +
83A ILE* 1.3 76.2 - - - +
85A GLU* 1.3 59.8 + - - +
87A MET* 3.4 9.0 + - - +
88A VAL* 2.9 55.1 + - + +
107A PHE* 5.3 1.6 - + - -
115A ALA* 4.0 5.8 - - + +
116A ALA 2.6 29.8 + - - -
117A ALA* 4.6 0.9 - - - -
118A GLN* 3.4 46.9 - - + +
121A THR* 2.8 31.7 + - - +
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Residues in contact with GLU 85 (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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81A SER 2.9 21.0 + - - +
82A SER* 3.6 6.3 - - - +
84A TYR* 1.3 76.6 - - - +
86A ALA* 1.3 59.6 + - - +
88A VAL* 3.4 7.3 + - - +
89A ARG* 2.9 30.5 + - - +
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Residues in contact with ALA 86 (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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42A VAL* 3.8 16.8 - - + -
43A HIS* 3.9 21.2 + - + -
46A ILE* 3.8 12.8 - - + -
82A SER 2.9 17.9 + - - +
83A ILE 3.4 4.7 - - - +
85A GLU* 1.3 77.2 - - - +
87A MET* 1.3 58.0 + - - +
89A ARG* 3.2 8.5 + - - +
90A MET* 2.9 31.3 + - - +
13E T 4.8 10.1 - - - +
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Residues in contact with MET 87 (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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46A ILE* 3.6 18.7 - - + +
50A MET* 3.6 25.4 - - + -
64A SER* 4.4 9.9 - - - +
67A ILE* 3.6 33.4 - - + -
68A THR* 3.6 26.9 - - + -
83A ILE* 2.9 14.9 + - + +
84A TYR* 3.7 9.0 - - + +
86A ALA* 1.3 73.4 - - - +
88A VAL* 1.3 65.5 + - - +
90A MET* 3.0 14.0 + - - +
91A ALA* 2.9 20.6 + - - +
101A VAL* 4.3 10.0 - - + +
107A PHE* 5.3 3.6 - - + -
123A ALA* 3.9 15.5 - - - -
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Residues in contact with VAL 88 (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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84A TYR* 2.9 54.9 + - + +
85A GLU* 3.7 7.0 - - - +
87A MET* 1.3 75.2 - - - +
89A ARG* 1.3 64.0 + - - +
91A ALA* 3.0 12.3 + - - +
92A GLN* 3.3 23.0 + - - +
107A PHE* 3.6 41.0 - - + +
115A ALA* 3.7 19.5 - - + +
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Residues in contact with ARG 89 (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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43A HIS* 4.8 0.4 - - + -
85A GLU 2.9 18.0 + - - +
86A ALA* 3.4 6.5 - - - +
88A VAL* 1.3 77.8 - - - +
90A MET* 1.3 58.1 + - - +
91A ALA 3.1 3.8 + - - -
92A GLN* 3.1 26.8 + - - +
95A SER* 3.7 25.1 + - - +
96A TYR* 3.2 46.1 + - + -
170A THR* 4.0 15.2 - - - +
263A TYR* 4.5 8.9 + - - -
264A MET* 5.4 2.6 - - - +
12E G 3.6 44.1 + - - -
13E T 3.6 30.9 + - - -
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Residues in contact with MET 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A HIS* 3.7 35.9 - - - +
46A ILE* 3.7 22.0 - - + -
47A LEU* 3.8 28.7 - - + -
86A ALA 2.9 14.8 + - - +
87A MET* 3.0 21.2 + - - +
89A ARG* 1.3 74.5 - - - +
91A ALA* 1.3 56.4 + - - +
92A GLN 3.5 0.2 - - - -
96A TYR* 3.5 33.8 - - + -
99A MET* 4.0 2.4 - - - -
100A LEU* 3.2 20.0 + - + -
101A VAL* 3.2 41.9 + - + -
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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