Contacts of the helix formed by residues 94 - 100 (chain A) in PDB entry 3GJ0
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 SER 94 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A ASP* 3.0 20.2 + - - +
92A VAL 3.4 1.0 - - - -
93A THR* 1.3 80.7 + - - +
95A ARG* 1.3 63.4 + - - +
96A VAL* 3.2 23.6 - - - +
97A THR* 2.8 40.9 + - - +
98A TYR 3.8 1.4 + - - -
131A VAL* 4.4 1.9 - - - +
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Residues in contact with ARG 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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93A THR 4.2 0.6 + - - -
94A SER* 1.3 71.8 + - - +
96A VAL* 1.3 64.7 + - - +
98A TYR* 3.0 7.1 + - - +
99A LYS* 3.0 27.4 + - + +
130A LYS* 3.1 58.1 + - + +
131A VAL* 3.8 15.5 - - + +
135A SER* 5.6 4.9 + - - -
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Residues in contact with VAL 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ASP* 4.9 1.6 - - - +
94A SER* 3.2 18.4 - - - +
95A ARG* 1.3 77.1 - - - +
97A THR* 1.3 70.6 + - + +
99A LYS* 3.1 11.4 + - + +
100A ASN* 3.0 38.2 + - - +
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Residues in contact with THR 97 (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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18A ASP* 3.5 24.0 + - + +
19A GLY 5.0 3.1 - - - +
20A GLY 6.1 0.2 - - - -
21A THR* 3.6 30.7 - - + -
89A MET 5.0 1.6 - - - +
90A PHE* 3.5 4.9 - - - +
91A ASP* 2.9 25.3 + - + -
94A SER* 2.8 35.3 + - - +
96A VAL* 1.3 81.0 - - + +
98A TYR* 1.3 61.2 + - - +
100A ASN* 3.5 9.5 + - - +
101A VAL* 3.6 14.9 + - - +
104A TRP* 5.5 1.2 - - - -
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Residues in contact with TYR 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A PHE* 3.8 39.7 - + + -
94A SER 3.8 0.6 + - - -
95A ARG 3.0 8.8 + - - +
97A THR* 1.3 79.1 + - - +
99A LYS* 1.3 88.6 + - + +
100A ASN 3.1 2.2 - - - -
101A VAL* 3.1 23.7 + - + +
102A PRO* 3.7 4.2 - - + +
119A LEU* 4.6 3.8 - - + -
131A VAL* 4.3 18.8 - - + -
135A SER* 3.4 19.4 + - - -
136A ILE* 4.1 17.9 - - + -
137A VAL* 2.9 31.0 + - + +
138A PHE* 2.9 27.9 + - + +
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Residues in contact with LYS 99 (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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95A ARG* 3.0 19.7 + - + +
96A VAL* 3.1 14.8 + - + +
98A TYR* 1.3 99.0 - - + +
100A ASN* 1.3 62.2 + - - +
102A PRO* 3.3 17.2 - - - +
103A ASN* 4.7 3.3 - - - +
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Residues in contact with ASN 100 (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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18A ASP* 2.7 42.1 + - - +
96A VAL* 3.0 27.0 + - - +
97A THR 3.5 2.0 + - - +
98A TYR 3.1 0.4 - - - -
99A LYS* 1.3 78.5 - - - +
101A VAL* 1.3 64.1 + - - +
102A PRO 3.3 2.7 - - - -
103A ASN* 3.1 32.4 + - + +
104A TRP* 3.2 17.9 + - + +
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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