Contacts of the helix formed by residues 86 - 95 (chain A) in PDB entry 4B7B
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 VAL 86 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A VAL 4.4 0.9 - - - +
82A TYR* 2.9 57.7 + - + +
85A VAL* 1.3 73.2 - - + +
87A CYS* 1.3 59.0 + - - +
88A PRO* 3.3 3.6 - - - -
89A ILE* 2.8 21.3 + - - +
90A LEU* 2.9 18.4 + - + +
101A ILE* 4.0 18.4 - - + -
135A ILE* 3.8 35.9 - - + -
139A THR* 3.7 13.7 - - - +
261A LEU* 4.9 6.3 - - + -
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Residues in contact with CYS 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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82A TYR* 3.1 15.9 + - + +
83A ARG* 3.7 17.9 - - + +
86A VAL* 1.3 74.4 - - - +
88A PRO* 1.3 67.1 - - + +
90A LEU* 3.4 2.8 + - - +
91A ASP* 3.0 34.8 + - - +
142A GLN* 3.5 34.8 - - - -
146A LYS* 4.8 0.4 - - - -
1368A CD 2.5 30.3 - - - -
1383A CO 4.2 3.4 - - - -
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Residues in contact with PRO 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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83A ARG 3.7 11.9 - - - +
84A SER 3.8 14.1 - - - +
85A VAL 3.8 8.7 - - - +
86A VAL 3.3 4.7 - - - -
87A CYS* 1.3 96.5 - - + +
89A ILE* 1.3 61.0 + - + +
91A ASP* 3.3 24.9 - - - +
92A GLU* 3.6 14.7 - - - +
329A ARG* 4.0 19.3 + - - +
1368A CD 4.1 0.4 - - - -
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Residues in contact with ILE 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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85A VAL 3.5 11.7 - - - +
86A VAL 2.8 14.2 + - - +
88A PRO* 1.3 72.3 - - + +
90A LEU* 1.3 59.9 + - - +
91A ASP 3.2 1.6 - - - -
92A GLU* 3.0 5.0 + - - +
93A VAL* 2.9 27.7 + - + +
99A CYS* 3.4 29.8 - - + -
101A ILE* 3.6 33.7 - - + -
261A LEU* 4.5 7.0 - - + -
329A ARG* 4.1 27.1 - - + +
331A SER* 3.6 29.2 - - - +
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Residues in contact with LEU 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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82A TYR* 3.6 12.1 - - - +
86A VAL* 2.9 19.9 + - + +
87A CYS 4.0 5.4 - - - +
89A ILE* 1.3 69.1 - - - +
91A ASP* 1.3 56.8 + - - +
93A VAL* 4.0 20.6 - - + -
94A ILE* 2.7 54.1 + - + +
139A THR* 4.0 13.2 - - + +
142A GLN* 3.5 35.7 - - + +
143A ILE* 3.6 41.3 - - + +
146A LYS* 5.6 2.0 - - + +
243A ILE* 4.5 0.4 - - + -
261A LEU* 4.5 6.7 - - + +
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Residues in contact with ASP 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 CYS* 3.0 14.6 + - - +
88A PRO* 3.3 17.8 - - - +
89A ILE 3.2 0.2 - - - -
90A LEU* 1.3 76.0 - - - +
92A GLU* 1.3 68.5 + - - +
94A ILE* 3.5 7.1 + - - +
95A MET* 3.2 28.6 + - - +
146A LYS* 3.2 22.1 + - - +
1368A CD 2.5 29.9 - - - -
1383A CO 4.1 2.8 + - - -
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Residues in contact with GLU 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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88A PRO 3.6 7.0 - - - +
89A ILE 3.0 8.0 + - - +
91A ASP* 1.3 82.9 - - - +
93A VAL* 1.3 66.5 + - - +
95A MET* 3.0 43.0 + - - +
96A GLY 3.3 0.3 + - - -
97A TYR* 3.1 34.1 + - + -
99A CYS* 4.2 14.4 - - - -
328A THR* 6.1 1.1 - - - -
329A ARG* 3.0 48.9 + - + +
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Residues in contact with VAL 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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89A ILE 2.9 18.3 + - - +
90A LEU* 3.2 15.9 + - + +
92A GLU* 1.3 74.3 - - - +
94A ILE* 1.3 57.1 + - - +
96A GLY 3.0 14.9 + - - -
97A TYR 3.5 7.9 - - - -
99A CYS* 3.8 18.6 - - + -
241A VAL 5.6 0.2 - - - +
243A ILE* 4.0 19.0 - - + +
245A MET* 4.1 0.9 - - - +
259A GLY* 3.1 24.5 + - - -
260A LYS* 3.5 40.2 - - - +
261A LEU* 3.8 18.8 - - + +
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Residues in contact with ILE 94 (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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90A LEU* 2.7 44.8 + - + +
91A ASP* 3.8 6.5 - - - +
93A VAL* 1.3 69.3 - - - +
95A MET* 1.3 61.5 + - + +
96A GLY 3.1 5.6 + - - -
143A ILE* 5.1 4.7 - - - -
146A LYS* 4.0 32.3 - - + +
147A LEU* 4.1 31.9 - - + -
150A ASN* 5.6 3.8 - - - +
243A ILE* 4.7 8.3 - - + -
245A MET* 3.3 25.6 - - - +
257A LYS* 4.3 5.9 - - - +
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Residues in contact with MET 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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91A ASP* 3.2 16.0 + - - +
92A GLU* 3.0 44.6 + - - +
94A ILE* 1.3 77.4 - - + +
96A GLY* 1.3 59.6 + - - +
97A TYR* 3.9 19.7 - - + -
257A LYS* 4.0 26.1 - - - +
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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