Contacts of the strand formed by residues 162 - 171 (chain A) in PDB entry 1BGO
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 HIS 162 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A GLN* 4.0 0.4 - - - -
25A CYS* 3.5 9.1 - - + +
134A ALA* 3.5 1.9 - - - -
135A ILE* 3.0 39.5 + - + +
137A ALA* 3.5 27.6 - - + -
142A PHE* 4.9 0.2 - + - -
161A ASN* 1.3 79.7 - - - +
163A ALA* 1.3 78.0 + - - +
164A VAL* 4.5 3.3 - - + +
182A ASN* 2.9 29.1 + - - -
183A SER* 3.8 6.5 - - - -
184A TRP* 3.4 26.6 + + - -
300A I10 2.7 49.5 + - - +
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Residues in contact with ALA 163 (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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25A CYS* 3.5 24.4 - - - +
26A TRP* 3.5 25.1 - - - +
29A SER* 3.8 4.4 + - - -
68A MET* 3.4 31.9 - - - -
133A VAL 3.5 4.7 - - - -
134A ALA* 4.3 0.4 - - - +
162A HIS* 1.3 81.8 + - - +
164A VAL* 1.3 64.3 + - - +
183A SER* 4.8 2.8 + - - -
300A I10 3.7 8.4 - - + +
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Residues in contact with VAL 164 (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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29A SER* 2.5 29.5 + - - +
132A SER* 3.8 0.2 - - - -
133A VAL* 2.8 42.9 + - + +
135A ILE* 4.6 20.2 - - + -
142A PHE* 6.0 0.9 - - + -
162A HIS* 4.0 6.0 + - + +
163A ALA* 1.3 75.6 - - - +
165A LEU* 1.3 60.8 + - - +
180A ILE* 3.3 29.8 - - + -
181A LYS 2.8 24.2 - - - +
182A ASN* 3.8 22.7 - - - +
183A SER 5.0 0.2 - - - +
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Residues in contact with LEU 165 (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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13A VAL* 5.2 2.7 - - + -
28A PHE 5.6 0.4 - - - +
29A SER* 3.8 15.3 - - - +
32A GLY* 4.0 21.5 - - - +
33A ALA* 3.6 26.2 - - - +
130A PRO* 4.0 8.3 - - + -
131A VAL 3.6 27.6 - - - +
132A SER 4.0 0.2 - - - +
164A VAL* 1.3 86.9 - - - +
166A ALA* 1.3 66.1 + - - +
167A VAL* 3.4 21.0 + - + -
180A ILE* 3.2 6.6 - - - +
181A LYS* 2.9 53.2 + - + +
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Residues in contact with ALA 166 (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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121A LEU* 4.9 4.5 - - + -
125A VAL* 4.4 14.1 - - + +
129A GLY 4.6 0.2 - - - +
130A PRO* 3.1 8.1 - - - +
131A VAL* 2.8 52.0 + - + +
133A VAL* 4.0 18.0 - - + +
165A LEU* 1.3 69.4 - - - +
167A VAL* 1.3 60.1 + - - +
168A GLY 3.5 3.3 + - - +
178A TRP* 5.0 9.6 - - + -
179A ILE 3.6 5.4 - - - +
180A ILE* 3.9 11.9 - - + -
206A ILE* 5.7 0.4 - - + -
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Residues in contact with VAL 167 (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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6A ASP* 3.8 9.8 - - - +
7A TYR* 3.2 30.5 + - - +
8A ARG* 3.8 26.9 - - + -
13A VAL* 3.4 32.5 - - + -
125A VAL* 4.6 0.7 - - - -
130A PRO* 4.5 5.4 - - + -
165A LEU* 3.4 26.6 + - + +
166A ALA* 1.3 72.0 - - - +
168A GLY* 1.3 55.5 + - - +
179A ILE* 2.7 28.0 + - + +
181A LYS* 4.3 7.6 - - + +
193A TYR* 4.3 4.7 - - + -
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Residues in contact with GLY 168 (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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5A VAL* 3.2 16.6 - - - -
6A ASP* 4.5 0.7 - - - -
7A TYR* 4.7 0.2 - - - -
125A VAL* 3.8 18.1 - - - +
166A ALA* 3.5 3.2 - - - +
167A VAL* 1.3 79.1 + - - +
169A TYR* 1.3 64.8 + - - +
178A TRP* 3.6 9.4 - - - +
179A ILE* 3.0 25.5 + - - +
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Residues in contact with TYR 169 (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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2A PRO 2.8 30.9 + - - -
3A ASP 3.7 15.3 - - - -
4A SER* 3.3 4.1 - - - -
5A VAL* 2.9 53.4 + - + +
122A LYS* 3.4 38.7 - - + -
125A VAL* 4.1 8.3 - - + -
126A ALA* 3.2 27.3 - - - +
168A GLY* 1.3 76.2 - - - +
170A GLY* 1.3 60.3 + - - +
177A HIS* 3.2 21.8 - - - +
178A TRP* 3.7 25.6 - + + +
179A ILE* 4.2 5.6 - - - +
198A ARG* 3.8 16.8 - - - +
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Residues in contact with GLY 170 (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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3A ASP 4.0 7.4 - - - -
4A SER* 3.6 17.7 - - - -
169A TYR* 1.3 80.2 - - - +
171A ILE* 1.3 60.9 + - - -
176A LYS* 3.3 1.6 - - - -
177A HIS* 2.9 34.7 + - - -
198A ARG* 3.0 14.2 + - - -
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Residues in contact with ILE 171 (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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3A ASP 5.9 0.9 - - - +
4A SER* 5.0 2.6 - - - -
170A GLY* 1.3 76.3 - - - +
172A GLN* 1.3 62.6 + - - +
174A GLY* 3.5 30.5 - - - +
175A ASN 3.2 20.9 - - - +
176A LYS* 4.4 16.8 - - + -
177A HIS* 3.4 10.4 - - - -
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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