Contacts of the strand formed by residues 133 - 139 (chain A) in PDB entry 2HQQ
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 PHE 133 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A LYS* 3.8 12.2 + - - +
5A GLN* 3.3 47.1 - - + +
7A LEU* 3.7 32.8 - - + -
58A ALA* 3.8 10.5 - - + -
85A TYR* 3.9 19.5 - + - -
128A VAL* 3.5 30.3 - - + -
129A ASP 3.6 16.6 - - - -
130A LEU* 3.3 11.2 + - - +
131A THR 3.3 1.0 - - - -
132A GLN* 1.3 88.1 - - + +
134A LYS* 1.3 59.1 + - - +
135A TRP 4.0 9.9 - - - +
136A ILE* 4.1 12.3 - - + -
166A ILE* 3.3 21.2 - - - +
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Residues in contact with LYS 134 (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 GLU* 5.6 5.3 - - - +
4A LYS* 3.5 38.6 - - + +
5A GLN 3.0 10.4 + - - +
6A ILE* 4.5 15.5 - - + -
56A PRO* 6.1 1.3 - - - -
133A PHE* 1.3 73.4 - - - +
135A TRP* 1.3 67.2 + - + +
165A LYS 4.3 4.2 - - - +
166A ILE* 3.8 5.8 - - - +
167A ARG* 3.1 25.0 + - - +
269A SER* 4.5 23.6 + - - +
270A GLN* 4.9 9.7 - - - +
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Residues in contact with TRP 135 (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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5A GLN 3.8 1.6 + - - +
6A ILE* 3.4 24.0 - - + -
7A LEU 2.9 24.3 + - - -
133A PHE* 3.5 2.0 - - - +
134A LYS* 1.3 84.6 - - + +
136A ILE* 1.3 90.8 + - - +
137A HIS* 4.0 2.5 - - + -
166A ILE* 4.0 0.4 - - - +
167A ARG* 3.1 62.8 - - + -
168A VAL 4.8 0.4 - - - -
169A SER* 2.9 37.8 + - - +
188A VAL* 4.0 13.2 - - + -
265A ILE* 3.7 31.8 - - + +
268A LEU* 3.8 18.8 - - + -
269A SER* 3.8 30.1 - - - -
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Residues in contact with ILE 136 (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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7A LEU* 3.3 30.1 - - + +
9A VAL* 4.4 4.5 - - + -
125A PHE* 4.2 5.6 - - + -
130A LEU* 3.7 31.0 - - + -
133A PHE* 4.1 11.7 - - + -
135A TRP* 1.3 81.9 - - - +
137A HIS* 1.3 62.9 + - - +
138A ILE* 4.3 14.4 - - + -
153A ILE* 3.8 30.7 - - + -
166A ILE* 3.7 22.7 - - + -
167A ARG 2.9 7.4 + - - +
168A VAL* 3.3 8.3 - - + +
169A SER 3.0 23.2 + - - +
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Residues in contact with HIS 137 (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 ILE* 5.4 0.4 - - + -
7A LEU 2.8 12.7 + - - +
8A CYS* 3.3 19.5 - - - -
9A VAL* 2.8 32.1 + - - +
42A ASN* 6.2 0.4 - - - +
43A ALA* 4.6 14.1 - - + +
46A SER* 5.2 6.9 + - - -
135A TRP* 4.0 3.7 - - + +
136A ILE* 1.3 72.1 - - - +
138A ILE* 1.3 67.6 + - - +
139A GLU* 4.3 5.6 + - - +
169A SER* 2.7 31.8 + - - +
170A VAL 4.1 2.9 - - - -
171A GLU* 3.9 36.2 + - + +
190A PHE* 4.1 12.8 - + - -
261A ASN* 5.2 7.4 + - + +
265A ILE* 3.7 21.2 - - + +
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Residues in contact with ILE 138 (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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9A VAL* 3.7 15.9 - - + +
125A PHE* 5.5 1.1 - - + -
136A ILE* 4.3 12.8 - - + +
137A HIS* 1.3 81.5 + - - +
139A GLU* 1.3 60.8 + - - +
140A GLY* 3.4 2.2 + - - +
146A GLN* 3.4 40.4 - - + +
149A MET* 4.4 22.4 - - + -
150A LEU* 3.6 37.0 - - + -
153A ILE* 4.7 8.5 - - + -
169A SER 3.0 13.6 + - - +
170A VAL* 3.3 9.6 - - + +
171A GLU 3.0 24.6 + - - -
182A LEU* 5.7 2.0 - - + -
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Residues in contact with GLU 139 (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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9A VAL 2.9 18.7 + - - +
10A GLY* 4.1 3.0 - - - -
11A LEU* 3.6 24.5 + - - +
41A GLY* 5.6 0.2 - - - -
42A ASN* 3.5 25.5 + - + +
43A ALA* 3.1 27.2 + - + +
137A HIS* 4.2 7.8 + - - +
138A ILE* 1.3 69.8 - - - +
140A GLY* 1.3 71.5 + - - +
141A ARG* 3.2 11.1 + - + +
146A GLN* 2.9 18.8 + - - -
171A GLU* 4.0 18.6 - - - +
173A GLU* 5.3 0.9 - - + +
174A LYS* 5.7 4.3 - - - -
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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