Contacts of the helix formed by residues 89 - 95 (chain J) in PDB entry 3EXG
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 ALA 89 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59J GLU* 3.7 17.7 - - + +
60J MET* 3.8 8.1 - - - +
63J ALA* 3.4 28.0 - - + -
80J PHE* 4.1 14.1 - - + -
86J SER 2.7 15.9 + - - +
88J GLN* 1.3 72.6 - - - +
90J ILE* 1.3 61.7 + - - +
91J ASP 3.1 3.6 - - - -
92J GLN* 3.1 16.5 + - - +
93J VAL* 3.3 12.0 + - - +
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Residues in contact with ILE 90 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86J SER* 3.0 9.7 + - - +
87J MET* 3.3 20.5 + - + +
88J GLN 3.6 0.4 - - - -
89J ALA* 1.3 79.1 - - - +
91J ASP* 1.3 59.2 - - - +
93J VAL* 3.3 6.0 + - - -
94J ILE* 3.0 37.4 + - + +
132J PHE* 5.5 0.2 - - + -
135J TRP* 4.1 19.5 - - + -
136J TYR* 3.6 38.1 - - + +
87L MET* 3.7 24.9 - - + +
90L ILE* 3.9 11.7 - - + -
135L TRP* 3.8 24.5 - - + -
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Residues in contact with ASP 91 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137I ILE* 3.5 27.8 - - - +
140I ALA* 4.1 14.1 - - - +
174I GLN* 4.2 10.7 + - - -
60J MET* 4.3 20.1 - - + +
89J ALA 3.1 0.6 - - - -
90J ILE* 1.3 79.6 - - - +
92J GLN* 1.3 62.0 + - - +
95J ASN* 2.9 53.5 + - - +
96J SER* 3.5 1.5 + - - -
84L ASN 5.3 0.2 - - - +
87L MET* 3.9 25.7 + - + +
88L GLN* 4.4 7.5 - - + +
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Residues in contact with GLN 92 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140I ALA* 3.3 18.8 + - - +
143I PRO* 4.0 3.2 - - - +
144I LEU* 3.9 8.9 - - - +
174I GLN* 3.0 27.1 + - - -
60J MET* 3.8 20.5 + - - +
63J ALA* 4.2 6.5 - - + -
64J GLY* 3.6 35.9 - - - +
67J VAL* 4.1 7.5 - - + +
89J ALA 3.1 8.6 + - - +
91J ASP* 1.3 80.3 + - - +
93J VAL* 1.3 59.7 + - + +
96J SER* 2.5 38.0 + - - -
97J ALA* 3.0 28.1 + - - +
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Residues in contact with VAL 93 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63J ALA* 5.3 0.4 - - + -
80J PHE* 4.9 8.1 - - + -
86J SER* 5.8 0.4 - - - +
89J ALA 3.7 13.0 - - - +
90J ILE* 3.3 12.5 + - - +
91J ASP 3.2 0.4 - - - -
92J GLN* 1.3 79.1 - - + +
94J ILE* 1.3 66.5 + - + +
97J ALA* 3.3 5.2 - - - +
98J ALA* 3.1 24.8 + - - +
114J PHE* 3.5 48.7 - - + -
136J TYR* 4.0 27.4 - - + +
142J LEU* 4.2 13.4 - - + +
168J VAL* 4.6 1.3 - - + -
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Residues in contact with ILE 94 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90J ILE* 3.0 18.3 + - + +
93J VAL* 1.3 81.4 - - + +
95J ASN* 1.3 66.5 + - - +
98J ALA* 3.4 21.5 + - + +
99J LYS* 3.4 23.6 + - - +
136J TYR* 4.5 6.3 - - + -
139J CYS* 3.4 37.0 - - + -
142J LEU* 4.0 16.6 - - + -
87L MET* 4.1 8.5 - - - -
130L GLN* 3.7 24.2 - - - +
135L TRP* 4.1 21.3 - - + -
266L TRP* 5.0 0.2 - - + -
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Residues in contact with ASN 95 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137I ILE* 3.3 23.5 - - + +
91J ASP* 2.9 31.0 + - - +
94J ILE* 1.3 77.1 - - - +
96J SER* 1.3 61.1 + - - +
99J LYS* 2.9 36.7 + - - +
103J MET* 4.2 7.4 - - - +
84L ASN 4.5 1.0 + - - -
87L MET* 2.8 29.4 - - - +
127L GLN* 2.7 46.2 + - - +
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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