Contacts of the strand formed by residues 178 - 187 (chain G) in PDB entry 6XAV
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 178 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139G THR* 2.5 45.8 + - + +
140G GLY 3.3 6.7 - - - +
141G VAL* 4.8 13.0 - - + +
173G PHE* 5.2 2.3 - - - -
176G GLY 5.4 2.2 - - - +
177G ASP* 1.3 76.4 - - - +
179G VAL* 1.3 62.4 + - - +
180G ARG* 4.3 2.9 + - + +
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Residues in contact with VAL 179 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138G ILE 3.6 0.9 - - - +
139G THR* 3.3 6.5 - - - -
140G GLY 2.7 35.2 + - - +
142G VAL* 3.7 24.2 - - + -
150G ILE* 4.8 2.7 - - + -
152G LEU* 3.8 12.2 - - + +
162G ILE* 3.8 22.0 - - + -
173G PHE* 3.6 36.6 - - + -
177G ASP 3.8 2.9 - - - +
178G ARG* 1.3 77.4 - - - +
180G ARG* 1.3 64.7 + - - +
181G GLY 3.8 0.5 + - - -
199G ARG* 3.4 23.6 - - - +
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Residues in contact with ARG 180 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137G ILE* 3.4 45.6 - - + +
138G ILE 3.6 5.2 - - - +
139G THR* 4.3 20.2 - - + +
178G ARG 4.3 2.7 + - - +
179G VAL* 1.3 74.6 - - - +
181G GLY* 1.3 58.9 + - - +
199G ARG* 3.0 28.7 + - - +
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Residues in contact with GLY 181 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137G ILE* 4.6 5.6 - - - +
138G ILE* 3.3 36.8 + - - +
152G LEU* 5.5 3.1 - - - +
162G ILE* 5.0 6.2 - - - +
179G VAL 3.8 1.8 + - - -
180G ARG* 1.3 75.6 - - - +
182G VAL* 1.3 60.4 + - - -
197G VAL* 3.5 19.7 - - - +
198G THR 5.0 2.7 - - - -
199G ARG* 5.0 4.5 - - - -
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Residues in contact with VAL 182 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88F ARG* 6.4 0.2 - - - +
134G GLU* 4.1 10.1 - - - +
135G GLY* 6.4 0.9 - - - -
136G GLU 5.3 11.2 - - - +
137G ILE* 5.3 13.5 - - + +
138G ILE* 5.4 0.7 - - - -
181G GLY* 1.3 72.6 - - - -
183G LEU* 1.3 76.3 + - + +
184G TYR* 4.0 0.8 + - + +
197G VAL* 3.4 5.1 - - - +
198G THR* 3.0 33.8 + - + +
199G ARG* 5.7 3.1 - - - +
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Residues in contact with LEU 183 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130G PHE* 4.5 22.7 - - + -
131G ARG* 3.4 35.3 + - - +
134G GLU* 3.2 46.8 - - + +
136G GLU 5.8 2.5 - - - +
138G ILE* 4.6 9.9 - - + -
181G GLY 4.1 0.6 + - - -
182G VAL* 1.3 81.9 - - + +
184G TYR* 1.3 60.5 + - - +
185G SER 5.4 0.2 - - - +
195G LEU* 3.8 32.8 - - + -
196G PHE 3.7 17.0 - - - +
197G VAL* 3.7 16.8 - - + +
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Residues in contact with TYR 184 (chain G).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84F SER* 4.8 12.6 + - - -
85F GLN* 3.8 19.2 + - + -
88F ARG* 5.1 17.7 - - - -
113F LEU 5.4 0.4 - - - -
114F LEU* 3.1 43.3 + - + +
131G ARG* 4.3 8.3 + - - +
182G VAL* 4.0 1.5 + - + +
183G LEU* 1.3 76.1 - - - +
185G SER* 1.3 73.1 + - - +
196G PHE 3.8 3.0 + - - -
198G THR* 4.3 21.3 - - + +
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Residues in contact with SER 185 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102F ARG* 5.3 11.7 - - - -
131G ARG* 3.9 10.1 + - - +
183G LEU* 5.1 0.2 - - - +
184G TYR* 1.3 92.6 - - - +
186G VAL* 1.3 64.6 + - - +
187G ARG* 4.3 10.2 + - - +
195G LEU* 4.3 0.3 - - - -
196G PHE* 2.9 34.3 + - - +
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Residues in contact with VAL 186 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108F GLU* 3.8 10.9 - - - +
127G VAL* 5.1 8.3 - - + -
131G ARG* 3.8 18.2 - - - +
185G SER* 1.3 76.0 - - - +
187G ARG* 1.3 68.5 + - - +
188G PRO* 4.1 0.5 - - - +
193G ALA* 3.9 15.5 - - + -
194G GLN 3.3 27.8 - - - +
195G LEU* 3.7 21.5 - - + -
196G PHE 4.2 0.2 - - - +
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Residues in contact with ARG 187 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102F ARG* 5.8 2.9 - - - +
105F LYS* 3.4 45.6 - - + +
108F GLU* 4.3 2.0 - - - +
185G SER* 5.2 9.6 + - - +
186G VAL* 1.3 75.8 - - - +
188G PRO* 1.3 69.1 - - + +
189G GLU* 2.8 13.6 + - - +
193G ALA* 3.5 12.5 - - - +
194G GLN 3.7 11.4 + - - +
196G PHE* 3.5 37.9 - - + -
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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