Contacts of the helix formed by residues 82 - 93 (chain A) in PDB entry 3O9Z
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 LEU 82 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78A SER* 3.6 11.7 - - - +
79A PRO* 2.9 19.0 + - + +
81A HIS* 1.3 104.6 - - + +
83A HIS* 1.3 63.5 + - - +
84A TYR 3.4 0.7 - - - -
85A PRO* 3.6 13.2 - - + -
86A GLN* 3.0 29.3 + - - +
311A NAD 3.4 37.7 - - + +
53D GLU* 3.9 26.5 - - + +
55D GLU* 3.8 30.5 - - + +
56D ALA* 5.6 0.2 - - + -
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Residues in contact with HIS 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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76A ILE* 3.6 12.7 - - + +
78A SER* 2.7 32.7 + - - -
79A PRO 3.3 13.8 + - - -
80A ASN* 3.0 20.6 + - - +
82A LEU* 1.3 77.9 - - - +
84A TYR* 1.3 55.1 + - - +
86A GLN* 3.7 0.7 - - - +
87A ILE* 2.8 41.6 + - - +
99A SER* 3.2 9.1 + - - +
100A GLU* 3.2 27.4 + - + +
101A LYS 3.5 4.3 - - - -
102A PRO 2.8 22.4 + - - -
103A LEU 3.1 16.8 - - - +
104A VAL* 4.6 0.4 - - - -
311A NAD 2.9 19.4 + - - -
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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
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80A ASN 4.5 1.2 + - - -
81A HIS 4.2 1.9 + - - +
83A HIS* 1.3 79.7 - - - +
85A PRO* 1.4 70.5 - - + +
87A ILE* 3.2 4.5 + - - +
88A ARG* 2.7 66.7 + - + +
104A VAL* 3.8 13.9 - - + +
105A LEU 5.6 0.2 - - - +
109A GLU* 3.4 64.6 - - + +
112A ARG* 3.4 23.2 - - + +
113A LEU* 3.7 30.5 - - + -
59D ALA* 4.7 7.2 - - + -
63D ASP* 4.5 4.7 + - - -
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Residues in contact with PRO 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 HIS 3.3 18.8 - - - +
82A LEU* 3.5 22.7 - - + +
84A TYR* 1.4 102.6 - - + +
86A GLN* 1.3 54.7 + - - +
87A ILE 3.4 0.2 - - - -
88A ARG* 3.4 13.1 + - + +
89A MET* 3.0 24.1 + - - +
92A ARG* 4.8 1.7 + - - -
109A GLU* 5.4 0.2 - - - +
55D GLU* 3.4 36.0 - - + +
56D ALA* 3.8 17.9 - - + +
59D ALA* 4.2 6.1 - - + -
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Residues in contact with GLN 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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7A THR* 2.8 22.1 + - - +
32A LEU* 3.8 8.7 - - - +
74A LEU* 3.5 10.4 - - + +
76A ILE* 3.5 16.6 - - + +
78A SER* 2.8 28.1 + - - -
82A LEU* 3.0 21.7 + - + +
85A PRO* 1.3 73.1 - - - +
87A ILE* 1.3 61.0 + - - +
88A ARG 3.3 0.2 - - - -
89A MET* 3.3 17.6 + - + +
90A ALA 3.0 22.2 + - - -
311A NAD 3.1 26.5 + - - -
55D GLU* 2.8 32.5 + - + +
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Residues in contact with ILE 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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76A ILE* 3.6 17.0 - - + -
83A HIS 2.8 27.5 + - - +
84A TYR 3.5 3.4 - - - +
86A GLN* 1.3 70.9 - - - +
88A ARG* 1.3 65.5 + - - +
90A ALA* 3.2 5.7 + - - +
91A LEU* 3.0 24.1 + - + +
97A ALA* 4.0 13.2 - - + -
99A SER* 4.1 5.2 - - - -
103A LEU* 3.6 38.6 - - + +
104A VAL* 3.9 11.7 - - + -
113A LEU* 3.6 26.5 - - + -
124A VAL* 3.7 24.9 - - + -
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Residues in contact with ARG 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* 2.7 70.5 + - + +
85A PRO* 3.5 12.6 - - + +
86A GLN 3.3 0.4 - - - -
87A ILE* 1.3 74.8 - - - +
89A MET* 1.3 62.7 + - - +
91A LEU* 3.4 6.7 + - - +
92A ARG* 3.0 38.2 + - - +
112A ARG* 5.2 0.6 - - - +
113A LEU* 4.1 4.0 - - + -
116A LEU* 2.8 38.8 - - - +
59D ALA* 3.2 21.3 + - + +
62D GLU* 2.7 33.8 + - - +
63D ASP* 2.8 35.5 + - - -
66D ASP* 4.8 3.0 + - - -
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Residues in contact with MET 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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7A THR* 4.6 0.4 - - + -
32A LEU* 4.5 2.9 - - + -
54A PRO 4.5 4.7 - - - +
57A PHE* 3.9 32.5 - - + -
58A GLU* 3.8 32.5 - - - +
74A LEU* 4.1 11.7 - - + -
85A PRO 3.0 13.6 + - - +
86A GLN* 3.4 33.0 - - + +
87A ILE 3.2 0.2 - - - -
88A ARG* 1.3 73.3 - - - +
90A ALA* 1.3 67.3 + - - +
92A ARG* 3.3 18.9 + - - +
93A LEU* 3.0 44.0 + - + +
55D GLU* 4.4 15.7 - - + -
58D GLU* 5.7 0.4 - - - +
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Residues in contact with ALA 90 (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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74A LEU* 3.7 29.8 - - + +
86A GLN 3.0 14.4 + - - +
87A ILE 3.2 8.3 + - - +
89A MET* 1.3 74.6 - - - +
91A LEU* 1.3 65.4 + - + +
93A LEU* 3.1 13.7 + - - +
94A GLY 3.2 0.2 + - - -
95A ALA* 3.0 28.2 + - - +
96A ASN 3.8 14.6 - - - +
97A ALA* 4.0 11.9 - - + -
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Residues in contact with LEU 91 (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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87A ILE* 3.0 26.8 + - + +
88A ARG* 4.0 5.2 - - - +
90A ALA* 1.3 81.2 - - + +
92A ARG* 1.3 62.2 + - - +
94A GLY* 3.1 12.8 + - - -
95A ALA 3.6 9.6 - - - +
96A ASN* 4.8 0.7 - - - -
97A ALA 5.0 0.9 - - - +
113A LEU* 4.3 8.3 - - + +
116A LEU* 3.9 34.8 - - + -
117A GLU 4.2 3.1 - - - +
120A THR* 3.6 30.1 - - + +
122A ARG* 3.6 28.0 - - + +
123A ARG 4.2 6.3 - - - +
124A VAL* 4.1 29.4 - - + -
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Residues in contact with ARG 92 (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 GLU* 2.8 36.7 + - - +
65A ARG* 3.3 17.8 + - - -
85A PRO 4.8 2.2 + - - -
88A ARG* 3.0 31.5 + - - +
89A MET* 3.3 25.1 + - - +
91A LEU* 1.3 77.5 - - - +
93A LEU* 1.3 60.1 + - + +
94A GLY 3.2 1.9 + - - -
120A THR* 4.7 4.7 - - - +
55D GLU* 5.0 2.4 + - - +
58D GLU* 3.3 29.5 + - - +
59D ALA* 4.0 11.7 - - - +
62D GLU* 2.8 46.9 + - - +
92D ARG* 3.6 24.9 - - - +
93D LEU* 6.1 0.6 - - - +
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Residues in contact with LEU 93 (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 GLU* 3.5 21.5 - - + +
61A LEU* 3.7 33.8 - - + +
62A GLU* 3.5 42.6 - - + +
65A ARG* 3.4 29.5 - - - +
71A VAL* 5.4 3.7 - - + +
74A LEU* 5.9 1.1 - - + -
89A MET* 3.0 41.9 + - + +
90A ALA* 3.1 7.8 + - - +
92A ARG* 1.3 78.5 - - + +
94A GLY* 1.3 61.9 + - - +
95A ALA* 3.4 5.6 - - + +
92D ARG* 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