Contacts of the strand formed by residues 94 - 100 (chain C) in PDB entry 6GJH
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 ARG 94 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C ALA 4.5 5.3 + - - +
93C ASP* 1.3 81.8 - - - +
95C TRP* 1.3 60.4 + - - +
96C ARG* 4.0 15.6 + - - +
166C GLU* 2.4 47.9 + - + +
167C ALA 3.4 11.4 - - - +
168C PRO* 4.2 9.9 - - + -
169C MET* 4.4 3.8 - - - -
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Residues in contact with TRP 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B SER 5.0 4.4 + - - -
156B SER* 4.7 16.5 - - - -
94C ARG* 1.3 70.7 - - - +
96C ARG* 1.3 64.6 + - - +
97C VAL* 3.4 37.2 - - + +
118C VAL* 4.6 6.3 - - + -
142C TYR* 4.2 21.1 - + + -
143C THR 4.6 8.4 + - - -
144C LEU* 3.5 30.7 - - + -
145C PRO* 3.6 29.5 - - + +
148C VAL* 5.5 1.3 - - + -
153C VAL* 5.5 0.2 - - + -
165C VAL* 4.0 28.3 - - + -
166C GLU* 3.2 9.6 - - - +
167C ALA* 2.7 47.6 + - + +
169C MET* 4.1 20.2 - - - +
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Residues in contact with ARG 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C ARG* 4.0 13.4 + - - +
95C TRP* 1.3 84.2 + - - +
97C VAL* 1.3 76.4 + - - +
98C SER* 4.9 6.1 + - - -
164C THR* 3.5 37.0 + - + +
165C VAL 3.3 6.5 - - - +
166C GLU* 3.3 29.1 + - + +
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Residues in contact with VAL 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C TRP* 3.4 32.8 - - + +
96C ARG* 1.3 82.0 - - - +
98C SER* 1.3 63.0 + - - +
99C LEU* 6.2 0.4 - - + -
120C ILE* 5.4 0.2 - - + -
142C TYR* 4.0 42.6 - - + +
163C LEU 4.0 0.3 - - - +
164C THR* 3.4 5.0 - - - +
165C VAL* 2.9 55.3 + - + +
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Residues in contact with SER 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C ARG* 4.8 7.8 + - - +
97C VAL* 1.3 74.8 + - - +
99C LEU* 1.3 63.8 + - - +
142C TYR* 4.2 8.5 + - - -
162C THR* 4.3 12.7 - - - +
163C LEU 3.3 7.4 - - - -
164C THR* 3.5 18.0 + - - +
131D HIS* 5.9 2.6 - - - -
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Residues in contact with LEU 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97C VAL* 6.2 0.7 - - + -
98C SER* 1.3 76.5 - - - +
100C ASP* 1.3 66.5 + - - +
101C VAL* 3.6 22.5 + - + +
120C ILE* 4.4 23.3 - - + -
138C PHE* 4.2 17.7 - - + -
140C ARG* 3.7 40.2 - - + +
142C TYR* 4.1 9.4 - - + +
162C THR* 4.4 3.7 - - - +
163C LEU* 2.7 47.5 + - + +
131D HIS* 5.7 6.5 - - + +
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Residues in contact with ASP 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99C LEU* 1.3 79.4 - - - +
101C VAL* 1.3 64.6 + - - +
102C ASN* 2.7 31.0 + - - +
160C GLU 4.2 3.5 - - - +
161C GLY 3.4 15.8 - - - +
162C THR* 4.0 13.9 + - + +
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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