Contacts of the strand formed by residues 180 - 189 (chain A) in PDB entry 6O4P
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 GLY 180 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90A PRO* 5.5 0.7 - - - -
91A PRO* 3.5 8.8 - - - +
176A VAL* 3.5 4.0 - - - +
177A ASN* 3.0 31.3 + - - +
178A PRO 3.7 0.6 - - - -
179A LEU* 1.3 78.8 - - - +
181A ALA* 1.3 60.2 - - - +
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Residues in contact with ALA 181 (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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91A PRO* 3.5 7.4 - - - +
174A THR* 3.9 9.2 - - + -
175A GLU 3.4 6.3 - - - -
176A VAL* 3.6 20.4 - - + -
180A GLY* 1.3 73.9 - - - -
182A SER* 1.3 64.1 + - - +
183A THR* 5.4 2.0 - - - +
408A SO4 4.0 9.7 + - - -
2C NAG 4.0 14.1 - - - +
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Residues in contact with SER 182 (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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91A PRO* 3.3 27.3 + - - -
92A ALA* 3.1 16.0 - - - -
93A ARG* 2.9 24.1 + - - +
94A PRO* 3.8 4.0 - - - +
173A VAL 3.8 1.4 - - - +
174A THR* 3.2 2.9 - - - -
175A GLU 2.8 34.9 + - - -
181A ALA* 1.3 74.0 - - - +
183A THR* 1.3 62.1 + - - +
408A SO4 3.0 16.6 + - - -
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Residues in contact with THR 183 (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 ARG* 3.7 12.4 - - - -
172A ASN* 3.2 30.5 - - - +
173A VAL 3.9 2.7 - - - -
174A THR* 3.2 15.6 + - - +
181A ALA* 5.4 1.6 - - - +
182A SER* 1.3 73.3 + - - +
184A ARG* 1.3 59.2 + - - +
185A LEU* 4.1 17.7 - - + -
406A SO4 3.5 16.8 + - - -
408A SO4 3.6 19.2 + - - -
1C NAG 3.8 21.2 - - - +
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Residues in contact with ARG 184 (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 ARG* 3.3 43.7 + - + +
94A PRO* 2.8 34.4 + - + +
95A VAL* 4.6 12.0 - - - +
96A VAL* 3.6 22.9 - - + +
113A SER* 4.9 2.0 - - - -
171A ILE 3.2 4.7 - - - +
172A ASN* 3.7 0.3 - - - -
173A VAL* 3.0 36.5 + - - +
182A SER 4.0 0.6 + - - -
183A THR* 1.3 73.8 - - - +
185A LEU* 1.3 70.9 + - - +
186A LEU* 5.2 4.7 - - + +
406A SO4 3.5 11.5 + - - -
407A SO4 2.5 37.6 + - - -
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Residues in contact with LEU 185 (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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170A ARG* 3.8 46.2 - - + +
171A ILE 3.3 4.9 - - - -
172A ASN* 4.1 16.4 - - + -
183A THR* 4.1 11.0 - - + +
184A ARG* 1.3 82.5 - - - +
186A LEU* 1.3 64.1 + - - +
187A ASP 4.2 1.1 + - - -
406A SO4 2.8 33.8 + - - +
1C NAG 3.5 33.0 - - + +
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Residues in contact with LEU 186 (chain A).
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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96A VAL* 3.7 39.5 - - + +
97A SER* 4.3 0.7 - - - -
98A CYS* 3.9 33.0 - - - +
170A ARG* 4.2 0.4 - - - +
171A ILE* 2.9 40.7 + - + +
184A ARG* 5.2 5.8 - - + +
185A LEU* 1.3 77.7 - - - +
187A ASP* 1.3 72.0 + - - +
188A VAL* 3.3 16.5 + - + +
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Residues in contact with ASP 187 (chain A).
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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129A LYS* 2.8 20.0 + - - -
168A GLN* 4.0 14.9 - - - +
169A TYR 3.3 3.6 - - - +
170A ARG* 2.7 47.2 + - - +
185A LEU 4.2 0.4 - - - -
186A LEU* 1.3 77.1 - - - +
188A VAL* 1.3 60.9 + - - +
189A SER 4.4 0.2 + - - -
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Residues in contact with VAL 188 (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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98A CYS* 3.8 28.5 - - + -
106A PHE* 4.3 21.8 - - + -
168A GLN* 4.4 2.2 - - - +
169A TYR* 2.5 44.7 + - + +
171A ILE* 3.9 12.6 - - + -
186A LEU* 3.3 19.2 + - + +
187A ASP* 1.3 78.8 - - - +
189A SER* 1.3 62.5 + - - +
190A LEU* 4.6 1.1 - - - +
193A ILE* 3.6 34.1 - - + -
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Residues in contact with SER 189 (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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167A SER 4.1 11.9 - - - -
168A GLN* 4.3 19.5 - - - -
187A ASP 4.3 0.4 - - - -
188A VAL* 1.3 76.1 - - - +
190A LEU* 1.3 65.7 + - - +
191A GLN* 4.3 7.2 - - - +
192A SER* 3.0 31.0 + - - -
193A ILE* 3.5 13.4 + - - +
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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