Contacts of the helix formed by residues 86 - 95 (chain A) in PDB entry 3A9L
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 GLU 86 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ILE* 3.9 15.4 - - + +
14A GLU* 3.9 13.3 - - - +
25A ILE* 3.7 26.1 - - + +
64A TYR* 2.5 35.7 + - - +
66A PHE* 4.1 3.8 - - + -
84A PHE* 3.7 19.7 - - + -
85A ASP* 1.3 76.4 + - - +
87A PRO* 1.3 81.6 - - - +
88A MET* 2.9 27.6 + - - +
89A ALA* 2.8 23.4 + - - +
90A VAL* 3.1 18.5 + - - +
29B ARG* 5.8 0.3 + - - -
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Residues in contact with PRO 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ILE* 5.1 4.9 - - + -
11A GLU* 4.7 11.4 - - - +
14A GLU* 5.1 2.7 - - - +
85A ASP 3.4 8.7 - - - +
86A GLU* 1.3 93.1 - - + +
88A MET* 1.3 58.6 + - - +
90A VAL* 3.5 7.5 + - + +
91A CYS* 3.0 28.6 + - - +
91B CYS* 4.0 24.9 - - - -
95B LYS* 4.1 15.0 - - - +
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Residues in contact with MET 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ILE* 3.9 33.7 - - + -
27A VAL* 4.7 4.0 - - + -
64A TYR* 4.3 6.1 - - + -
86A GLU* 2.9 19.8 + - - +
87A PRO* 1.3 78.1 - - - +
89A ALA* 1.3 52.7 + - - +
91A CYS* 3.3 7.5 + - - +
92A MET* 2.8 38.0 + - - +
27B VAL* 4.2 13.2 - - + -
29B ARG* 4.7 3.6 - - + -
88B MET* 4.3 27.4 - - + +
91B CYS* 4.2 22.9 - - + -
92B MET* 4.0 37.2 - - - +
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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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37A PHE* 5.8 0.9 - - + -
64A TYR* 3.4 40.1 - - + +
84A PHE* 3.7 19.1 - - + -
86A GLU* 2.8 16.4 + - - +
88A MET* 1.3 74.4 - - - +
90A VAL* 1.3 51.9 + - - +
92A MET* 3.1 3.5 + - - +
93A LEU* 2.7 45.9 + - + +
152A ILE* 4.7 7.6 - - + -
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Residues in contact with VAL 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A ASP* 3.8 25.1 - - + +
86A GLU 3.1 15.2 + - - +
87A PRO* 3.8 8.1 - - + +
89A ALA* 1.3 71.0 - - - +
91A CYS* 1.3 67.1 + - - +
93A LEU* 4.1 3.0 - - - +
94A SER* 3.3 21.6 + - - -
152A ILE* 4.5 13.7 - - + -
155A ARG* 3.7 36.6 - - + +
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Residues in contact with CYS 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 PRO 3.0 18.7 + - - +
88A MET* 3.5 7.2 - - - +
90A VAL* 1.3 77.4 - - - +
92A MET* 1.3 61.3 + - - +
94A SER* 2.7 23.3 + - - -
95A LYS* 3.1 40.3 - - - +
86B GLU* 5.4 0.7 - - - -
87B PRO* 4.0 24.0 - - - -
88B MET* 4.5 15.3 - - + -
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Residues in contact with MET 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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27A VAL* 3.6 33.2 - - + -
29A ARG* 3.6 42.4 - - + -
35A ILE* 3.6 21.8 - - + -
62A SER* 4.0 4.9 - - - -
63A LEU 4.0 4.5 - - - +
64A TYR* 4.8 6.1 - - + -
88A MET 2.8 22.5 + - - +
89A ALA* 3.4 9.9 - - - +
91A CYS* 1.3 71.9 - - - +
93A LEU* 1.3 61.8 + - + +
95A LYS* 2.9 9.2 + - - -
96A HIS* 2.7 47.1 + - + -
88B MET* 3.8 12.3 - - - +
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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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35A ILE* 4.3 11.9 - - + -
37A PHE* 3.8 32.8 - - + -
64A TYR* 5.8 0.7 - - + -
89A ALA* 2.7 28.7 + - - +
90A VAL* 4.1 4.7 - - - +
91A CYS 3.4 0.2 - - - -
92A MET* 1.3 72.6 - - + +
94A SER* 1.3 57.2 + - - +
96A HIS* 3.1 20.6 + - - +
99A ALA* 3.4 32.3 - - + -
152A ILE* 3.7 35.2 - - + +
155A ARG* 3.4 15.0 - - + +
156A CYS* 3.1 28.8 - - + +
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Residues in contact with SER 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 VAL* 3.3 12.6 + - - -
91A CYS* 2.7 21.9 + - - -
93A LEU* 1.3 77.0 - - - +
95A LYS* 1.3 72.3 + - - +
96A HIS 3.3 2.3 + - - -
155A ARG 4.1 8.5 - - - -
156A CYS 4.7 0.2 - - - -
157A ALA* 3.8 19.4 - - - +
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Residues in contact with LYS 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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29A ARG* 3.7 43.1 + - - +
32A PRO* 3.6 12.3 - - - +
91A CYS* 3.1 40.5 - - - +
92A MET* 2.9 11.0 + - - +
94A SER* 1.3 89.7 + - - +
96A HIS* 1.3 65.3 + - + +
157A ALA* 5.3 0.9 - - - -
14B GLU* 4.4 15.5 - - - +
87B PRO* 4.7 8.5 - - - +
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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