Contacts of the strand formed by residues 120 - 128 (chain F) in PDB entry 2WJZ
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 120 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2E LEU* 3.3 19.4 - - + +
113F LEU* 3.9 10.1 - - + -
118F LEU* 3.9 5.1 - - - +
119F PRO* 1.3 69.3 - - - +
121F MET* 1.3 57.7 + - - +
124F ASN* 2.9 32.9 + - + +
139F PHE* 3.4 34.9 - + + +
140F VAL* 3.2 6.8 + - - -
141F HIS* 2.9 55.3 + - - +
156F THR* 4.4 0.7 - - + -
158F TYR* 3.2 50.9 - + + +
163F PHE* 4.2 8.6 - + - -
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Residues in contact with MET 121 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2E LEU* 3.2 24.3 - - - +
5E ARG* 5.6 5.1 + - - -
99E LYS* 5.1 13.7 - - - +
123E GLN* 4.8 17.3 - - - +
166E GLY* 3.9 23.6 - - - +
167E GLU* 5.6 3.6 - - + +
197E PRO* 4.0 19.1 - - + -
119F PRO* 3.2 27.3 + - + +
120F HIS* 1.3 81.7 - - - +
122F GLY* 1.3 63.3 + - - +
139F PHE 3.4 7.4 - - - +
140F VAL* 4.3 22.7 - - + -
158F TYR* 5.2 0.4 + - - -
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Residues in contact with GLY 122 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2E LEU* 4.2 6.9 - - - +
3E ALA 5.6 0.9 - - - -
5E ARG* 5.0 12.8 - - - -
46E GLU* 6.0 0.4 - - - -
121F MET* 1.3 77.4 - - - +
123F TRP* 1.3 69.8 + - - -
124F ASN 3.6 1.7 + - - -
138F ALA* 4.4 2.5 - - - -
139F PHE* 2.8 37.1 + - - +
140F VAL* 5.0 0.4 - - - +
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Residues in contact with TRP 123 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2E LEU* 3.4 3.9 - - - +
3E ALA* 2.9 42.3 + - + +
5E ARG* 4.2 15.9 - - + +
45E ASP* 3.1 44.2 + - + +
46E GLU* 4.8 3.4 - - + +
75E ILE* 4.0 9.2 - - + -
76E PRO* 4.0 5.9 - - + +
249E ARG* 3.4 41.1 - - - -
122F GLY* 1.3 72.2 - - - -
124F ASN* 1.3 60.2 + - - +
136F TYR* 3.4 32.6 - - + -
137F TYR 3.3 15.9 - - - -
138F ALA* 4.1 6.3 - - + +
181F ALA 3.4 10.5 - - - -
182F SER* 3.4 43.3 - - - -
183F SER* 3.8 9.4 - - - -
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Residues in contact with ASN 124 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1E MET* 3.0 26.9 + - - -
2E LEU* 3.5 9.8 - - + +
120F HIS* 2.9 42.0 + - + +
122F GLY 3.6 1.6 + - - -
123F TRP* 1.3 72.8 - - - +
125F GLU* 1.3 80.1 + - - +
126F VAL 3.5 0.2 + - - -
136F TYR* 3.5 7.2 - - - -
137F TYR 3.0 27.4 + - - -
139F PHE* 3.3 14.6 - - + -
156F THR* 3.5 9.9 - - + +
157F GLU 2.8 26.8 + - - +
158F TYR* 4.0 1.8 - - - +
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Residues in contact with GLU 125 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1E MET 4.6 8.0 + - - +
124F ASN* 1.3 83.0 + - - +
126F VAL* 1.3 55.9 + - - +
127F ILE* 3.8 30.4 - - + +
135F GLY* 3.6 16.4 - - - +
136F TYR* 3.6 35.3 + - + +
155F THR 3.5 3.5 - - - +
156F THR* 2.6 31.3 + - - +
157F GLU 4.6 0.7 + - - -
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Residues in contact with VAL 126 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125F GLU* 1.3 73.0 - - - +
127F ILE* 1.3 66.8 + - - +
128F PHE* 3.6 32.7 + - + -
134F ASN* 3.5 5.4 - - - -
135F GLY 2.9 29.0 + - - -
137F TYR* 3.6 27.1 - - + -
139F PHE* 3.4 24.7 - - + -
154F GLY* 4.1 7.0 - - - -
155F THR 3.3 2.5 - - - +
156F THR* 3.4 13.0 - - - +
165F SER* 3.4 15.3 - - - +
166F ALA* 4.8 0.2 - - + -
177F PHE* 3.7 11.0 - - + -
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Residues in contact with ILE 127 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125F GLU* 3.8 31.6 - - + +
126F VAL* 1.3 82.0 - - - +
128F PHE* 1.3 67.7 + - - +
129F LYS* 4.0 0.3 + - - +
134F ASN* 3.8 26.9 - - + +
153F LEU 4.0 0.2 - - - +
154F GLY* 3.3 1.8 - - - -
155F THR* 2.9 50.1 + - + +
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Residues in contact with PHE 128 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126F VAL* 3.6 23.1 - - + -
127F ILE* 1.3 80.6 - - - +
129F LYS* 1.3 64.7 + - - +
130F ASP* 3.3 11.0 + - - +
132F PHE* 3.5 43.3 - + + +
133F PRO 3.4 21.3 - - - -
134F ASN* 2.8 24.5 + - - +
137F TYR* 3.8 8.7 - + - -
153F LEU* 3.3 23.1 - - + -
154F GLY* 3.9 2.7 - - - -
166F ALA* 3.5 23.6 - - + -
175F PHE* 4.1 8.1 - + - -
177F PHE* 4.0 18.4 - + - -
189F LEU* 4.0 5.8 - - + -
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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