Contacts of the strand formed by residues 162 - 169 (chain G) in PDB entry 6H25
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 LEU 162 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A SER* 4.6 14.5 + - - +
9A CYS* 4.7 6.7 - - + -
118G ILE* 3.8 18.4 - - + -
119G GLY 3.2 12.6 - - - +
120G ILE* 4.6 6.0 - - + +
160G GLY 4.3 0.2 + - - -
161G ASP* 1.3 75.7 - - + +
163G ILE* 1.3 62.5 + - - +
192G VAL* 4.0 6.2 - - - +
193G ILE* 3.6 37.9 + - + -
194G GLY 3.4 25.8 - - - +
199G LEU* 3.8 28.3 - - + -
238G TRP* 3.9 26.9 - - + +
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Residues in contact with ILE 163 (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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117G VAL 3.5 2.6 - - - +
118G ILE* 3.5 4.0 - - - -
119G GLY* 2.9 35.4 + - - +
121G VAL* 3.7 24.0 - - + -
129G PHE* 4.4 0.4 - - + -
131G VAL* 5.5 3.1 - - + -
141G LEU* 4.1 21.3 - - + -
146G PHE* 3.9 19.1 - - + -
157G VAL* 4.2 15.0 - - + -
161G ASP* 4.0 6.5 - - + +
162G LEU* 1.3 79.8 - - - +
164G TYR* 1.3 62.0 + - - +
165G GLY 4.0 0.2 + - - -
178G MET* 4.5 7.2 - - + +
180G CYS* 3.6 27.4 - - - -
191G GLY 3.6 10.3 - - - +
192G VAL* 4.5 9.9 - - + -
193G ILE* 4.9 2.0 - - - +
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Residues in contact with TYR 164 (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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116G HIS* 3.3 45.8 + + + +
117G VAL 4.0 4.9 - - - -
118G ILE* 4.1 11.9 - - + +
163G ILE* 1.3 73.1 - - - +
165G GLY* 1.3 59.7 + - - +
180G CYS* 3.4 7.7 - - - -
188G ASN 5.5 2.9 - - - -
189G GLY 4.2 17.0 - - - -
190G MET* 3.6 18.3 - - + +
191G GLY 3.0 31.0 + - - +
193G ILE* 3.7 25.7 - - + +
230G VAL* 3.8 18.6 - - + -
231G PHE 3.5 21.5 + - - -
72K TYR 4.9 0.3 + - - -
73K GLY* 3.7 20.8 - - - -
74K ARG* 3.9 15.6 + - + -
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Residues in contact with GLY 165 (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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116G HIS* 3.5 7.0 + - - -
117G VAL 3.2 29.1 + - - -
164G TYR* 1.3 78.0 - - - +
166G GLN* 1.3 64.5 + - - +
178G MET* 3.7 14.6 - - - +
179G VAL 3.3 13.0 - - - -
180G CYS* 3.9 1.8 - - - -
190G MET* 4.4 11.9 - - - -
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Residues in contact with GLN 166 (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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114G GLY* 4.9 9.2 - - - -
115G ASP 3.3 19.5 - - - +
116G HIS* 3.6 20.3 + - - +
117G VAL* 5.1 0.4 - - - +
165G GLY* 1.3 75.4 - - - +
167G PHE* 1.3 67.1 - - - +
168G VAL* 5.5 2.9 - - + +
178G MET* 3.7 6.6 - - - +
179G VAL* 2.8 42.6 + - + +
181G ILE 3.9 12.1 + - - -
182G ASP* 4.9 5.7 - - - +
183G SER 5.5 1.0 - - - +
190G MET* 3.8 23.4 - - + +
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Residues in contact with PHE 167 (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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109G TYR* 4.0 14.4 - + - -
111G PRO* 5.4 4.9 - - + -
112G VAL 3.9 18.4 - - - +
113G LYS* 4.5 0.9 - - - +
114G GLY* 3.2 31.0 + - - +
115G ASP 3.8 11.7 + - - +
117G VAL* 3.6 29.2 - - + -
133G VAL* 3.6 29.8 - - + -
139G ALA* 3.9 23.3 - - + -
166G GLN* 1.3 76.6 - - - +
168G VAL* 1.3 61.7 + - - +
170G ALA* 4.4 12.6 - - + -
176G PRO* 4.2 17.5 - - + -
177G GLU 3.6 12.3 - - - +
178G MET* 3.7 20.4 - - + +
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Residues in contact with VAL 168 (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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113G LYS* 3.4 29.3 - - - +
166G GLN* 3.6 4.6 + - + +
167G PHE* 1.3 76.2 - - - +
169G VAL* 1.3 77.8 + - + +
177G GLU* 2.9 17.2 + - + +
178G MET 4.6 0.2 - - - -
179G VAL* 3.7 44.2 - - + -
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Residues in contact with VAL 169 (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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113G LYS* 5.4 0.9 - - - -
167G PHE* 4.5 0.5 - - - +
168G VAL* 1.3 89.3 + - + +
170G ALA* 1.3 64.0 + - - +
171G ASN* 5.3 4.5 - - - +
175G GLU 5.2 2.2 - - - +
176G PRO* 3.4 5.4 - - + +
177G GLU* 3.1 61.4 + - + +
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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