Contacts of the helix formed by residues 85 - 92 (chain A) in PDB entry 4A9J
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 85 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A TYR* 2.8 48.8 + - + +
84A LYS* 1.3 79.5 - - - +
86A VAL* 1.3 64.2 + - - +
87A MET 3.7 0.2 - - - -
88A LYS* 4.1 1.4 - - - +
89A ALA* 3.2 24.8 + - - +
176A LYS* 3.8 24.0 - - + +
97C TRP* 3.4 43.3 - - + -
100C ARG* 4.7 9.9 - - - +
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Residues in contact with VAL 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A TYR* 3.3 17.7 + - + -
82A LEU* 3.4 30.7 - - + +
85A VAL* 1.3 74.1 - - - +
87A MET* 1.3 66.7 + - - +
89A ALA* 3.2 4.4 + - - +
90A LEU* 3.0 35.0 + - + +
145A PHE* 4.1 10.8 - - + -
173A PHE* 3.7 34.1 - - + -
176A LYS* 3.6 30.1 - - + -
177A VAL* 4.5 2.9 - - + -
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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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82A LEU 2.8 21.3 + - - +
83A HIS* 3.6 12.3 - - + +
86A VAL* 1.3 70.6 - - - +
88A LYS* 1.3 61.0 + - - +
90A LEU* 4.5 0.9 - - - +
91A TRP* 2.8 49.3 + - + +
123A MET* 3.6 42.4 - - + +
126A ILE* 3.5 23.1 - - + -
127A LYS* 3.7 22.4 - - + +
130A LEU* 4.1 11.4 - - + -
145A PHE* 3.4 29.8 - - + -
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Residues in contact with LYS 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 HIS* 3.3 8.5 + - - +
84A LYS* 3.2 47.6 + - - +
85A VAL 4.1 1.1 - - - +
86A VAL 3.3 0.2 - - - -
87A MET* 1.3 80.0 - - - +
89A ALA* 1.3 60.6 + - - +
91A TRP* 4.3 3.1 - - - +
92A LYS* 3.4 33.9 + - + +
101C GLN* 4.1 20.4 + - - +
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Residues in contact with ALA 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 3.2 18.4 + - - +
86A VAL* 3.6 4.7 - - - +
88A LYS* 1.3 81.0 - - - +
90A LEU* 1.3 63.3 + - - +
92A LYS* 3.8 12.7 - - - +
93A HIS* 3.6 20.8 + - - +
172A ILE* 4.4 20.0 - - + -
176A LYS* 4.4 12.8 - - - -
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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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86A VAL* 3.0 29.2 + - + +
87A MET* 4.2 2.0 - - - +
89A ALA* 1.3 74.4 - - - +
91A TRP* 1.3 66.7 + - - +
93A HIS* 3.2 10.4 + - - +
96A ALA* 3.0 21.2 - - - +
123A MET* 3.6 19.8 - - + +
145A PHE* 3.5 33.4 - - + -
149A PHE* 4.5 5.4 - - + -
169A LEU* 3.3 37.3 - - + +
172A ILE* 3.8 25.1 - - + -
173A PHE* 4.1 13.5 - - + +
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Residues in contact with TRP 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 MET* 2.8 31.1 + - + +
88A LYS* 4.3 3.6 - - - +
90A LEU* 1.3 75.1 - - - +
92A LYS* 1.3 62.2 + - + +
96A ALA* 3.6 2.1 - - - +
100A ARG* 2.9 83.6 + - + +
123A MET* 3.8 18.5 - - + -
124A GLY* 3.7 27.8 - - - -
127A LYS* 3.9 35.8 - - + +
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Residues in contact with LYS 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 LYS* 3.4 26.6 + - + +
89A ALA* 3.8 11.2 - - - +
90A LEU 3.3 0.2 - - - -
91A TRP* 1.3 81.1 - - + +
93A HIS* 1.3 66.5 + - - +
94A GLN* 3.7 1.4 + - - -
100A ARG* 4.2 6.6 + - - +
1189A SO4 5.0 2.3 + - - -
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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