Contacts of the strand formed by residues 120 - 128 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A LEU* 3.1 27.1 - - + +
113B LEU* 3.9 8.7 - - + -
118B LEU* 3.9 5.3 - - - +
119B PRO* 1.3 69.4 - - - +
121B MET* 1.3 58.6 + - - +
124B ASN* 2.9 32.2 + - + +
139B PHE* 3.4 31.4 - + + +
140B VAL* 3.2 6.9 + - - -
141B HIS* 2.9 58.6 + - - +
156B THR* 4.4 0.4 - - + -
158B TYR* 3.2 42.8 - + + +
163B PHE* 4.2 8.8 - + - -
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Residues in contact with MET 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A LEU* 3.2 24.5 - - - +
5A ARG* 5.6 3.3 + - - -
99A LYS* 4.6 17.7 - - - +
123A GLN* 3.9 43.1 - - + +
166A GLY* 4.0 22.4 - - - +
167A GLU* 5.6 3.4 - - + +
197A PRO* 5.1 9.0 - - + -
119B PRO* 3.2 23.7 + - + +
120B HIS* 1.3 79.7 - - - +
122B GLY* 1.3 61.2 + - - +
139B PHE 3.4 7.0 - - - +
140B VAL* 4.4 13.9 - - + -
158B TYR* 5.2 0.6 - - - -
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Residues in contact with GLY 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A LEU* 4.4 7.9 - - - +
5A ARG* 5.0 11.7 - - - -
46A GLU* 5.5 2.9 - - - -
121B MET* 1.3 78.8 - - - +
123B TRP* 1.3 69.1 + - - -
124B ASN 3.6 1.2 + - - -
138B ALA* 4.4 2.5 - - - -
139B PHE* 2.8 37.0 + - - +
140B VAL* 5.0 0.2 - - - +
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Residues in contact with TRP 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A LEU* 3.4 4.7 - - - +
3A ALA* 2.9 38.8 + - + +
5A ARG* 4.2 16.8 - - + +
45A ASP* 2.8 43.0 + - + -
46A GLU* 4.5 3.1 - - + +
75A ILE* 3.7 14.6 - - + -
76A PRO* 4.0 9.4 - - + +
249A ARG* 3.3 42.8 - - + -
122B GLY* 1.3 75.0 - - - -
124B ASN* 1.3 59.6 + - - +
136B TYR* 3.4 34.1 - - + -
137B TYR 3.3 15.7 - - - -
138B ALA* 4.1 4.3 - - + -
181B ALA 3.4 11.2 - - - -
182B SER* 3.4 43.5 - - - -
183B SER 3.9 1.8 - - - -
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Residues in contact with ASN 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET 2.5 34.0 + - - -
2A LEU* 3.5 11.2 - - + +
120B HIS* 2.9 36.6 + - + +
122B GLY 3.6 1.4 + - - -
123B TRP* 1.3 73.7 - - - +
125B GLU* 1.3 74.2 + - - +
136B TYR* 3.5 7.4 - - - -
137B TYR 3.0 27.1 + - - -
139B PHE* 3.3 20.4 - - + -
156B THR* 3.5 9.0 - - + +
157B GLU 2.8 23.2 + - - +
158B TYR* 4.0 2.2 - - - +
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Residues in contact with GLU 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET 4.5 8.3 + - - +
124B ASN* 1.3 82.7 + - - +
126B VAL* 1.3 56.3 + - - +
127B ILE* 3.7 30.9 - - + +
135B GLY* 3.6 15.1 - - - +
136B TYR* 3.5 34.2 + - + +
155B THR 3.5 3.1 - - - +
156B THR* 2.7 31.3 + - - +
157B GLU 4.6 0.5 + - - -
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Residues in contact with VAL 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B GLU* 1.3 73.4 - - - +
127B ILE* 1.3 67.5 + - - +
128B PHE* 3.6 32.5 + - + -
134B ASN* 3.5 5.4 - - - -
135B GLY 2.9 29.0 + - - -
137B TYR* 3.6 26.9 - - + -
139B PHE* 3.4 34.5 - - + -
154B GLY* 4.1 6.5 - - - -
155B THR 3.3 2.7 - - - +
156B THR* 3.4 3.4 - - - +
165B SER* 3.4 16.2 - - - +
166B ALA* 4.8 0.2 - - + -
177B PHE* 3.7 11.4 - - + -
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Residues in contact with ILE 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B GLU* 3.7 33.0 - - + +
126B VAL* 1.3 83.1 - - - +
128B PHE* 1.3 67.2 + - - +
129B LYS* 5.8 0.2 - - - +
134B ASN* 3.8 26.5 - - + +
153B LEU 4.0 0.2 - - - +
154B GLY* 3.3 1.4 - - - -
155B THR* 2.8 50.1 + - + +
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Residues in contact with PHE 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B VAL* 3.6 22.4 - - + -
127B ILE* 1.3 79.0 - - - +
129B LYS* 1.3 64.3 + - - +
130B ASP* 3.3 10.6 + - - +
132B PHE* 3.5 39.9 - + + +
133B PRO 3.3 26.9 - - - -
134B ASN* 2.8 25.4 + - - +
137B TYR* 3.8 8.7 - + - -
153B LEU* 3.3 23.8 - - + -
154B GLY* 3.9 2.9 - - - -
166B ALA* 3.5 22.4 - - + -
175B PHE* 4.1 8.5 - + - -
177B PHE* 4.0 11.9 - + - -
189B LEU* 4.0 11.7 - - + -
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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