Contacts of the strand formed by residues 118 - 125 (chain B) in PDB entry 3WYR
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 ASN 118 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B ARG 3.9 0.9 - - - +
109B PRO* 3.8 18.5 - - - +
116B GLY 3.9 0.4 + - - -
117B GLU* 1.3 73.3 - - - +
119B VAL* 1.3 61.1 + - - +
120B THR* 4.2 3.8 + - - +
162B GLY* 3.1 12.0 - - - +
163B PRO* 3.2 25.1 - - - +
201B NAG 1.4 67.9 + - - +
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Residues in contact with VAL 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B ALA* 4.9 1.3 - - + -
108B ARG 3.5 10.5 - - - +
109B PRO* 5.2 1.1 - - + -
110B GLY 4.6 10.8 - - - +
113B VAL* 3.9 22.4 - - + -
117B GLU 3.6 11.0 - - - +
118B ASN* 1.3 76.2 - - - +
120B THR* 1.3 65.5 + - - +
121B LEU* 4.2 20.0 - - + -
161B LEU* 2.8 40.7 + - + +
162B GLY 2.9 10.3 + - - +
164B ALA* 4.4 10.1 - - + -
192B VAL* 4.5 23.8 - - + -
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Residues in contact with THR 120 (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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106B THR 4.2 0.2 - - - +
107B ALA 3.8 0.2 - - - -
108B ARG* 2.9 77.2 + - - +
118B ASN* 4.2 4.9 + - - +
119B VAL* 1.3 75.6 + - - +
121B LEU* 1.3 72.2 + - - +
122B SER* 4.6 0.9 + - - -
158B ASP* 4.0 8.1 - - + -
159B PHE 3.3 14.8 - - - +
160B PRO* 3.5 16.6 - - + +
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Residues in contact with LEU 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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105B LEU* 3.9 11.2 - - + -
106B THR 3.3 4.7 - - - +
107B ALA* 3.7 26.9 - - + -
119B VAL* 4.5 4.9 - - + -
120B THR* 1.3 74.7 - - - +
122B SER* 1.3 67.4 + - - +
134B LEU* 3.8 15.0 - - + -
158B ASP* 3.2 1.6 - - - -
159B PHE* 2.8 41.1 + - + +
161B LEU* 3.8 20.4 - - + -
170B TYR* 3.4 42.4 - - + -
190B LEU* 3.8 16.6 - - + -
192B VAL* 4.2 8.7 - - + -
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Residues in contact with SER 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B SER 3.3 1.9 - - - +
105B LEU* 3.3 9.2 - - - -
106B THR* 2.9 48.0 + - - -
108B ARG* 4.2 12.2 + - - +
120B THR 4.6 0.7 + - - -
121B LEU* 1.3 76.1 + - - +
123B CYS* 1.3 60.3 + - - +
124B SER* 4.0 1.8 + - - -
156B GLN* 3.5 18.9 + - - -
157B ALA 3.3 4.7 - - - -
158B ASP* 2.4 30.6 + - - +
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Residues in contact with CYS 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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103B PRO* 4.6 0.2 - - + -
104B SER 3.3 3.4 - - - -
105B LEU* 3.7 11.4 - - - -
122B SER* 1.3 69.2 - - - +
124B SER* 1.3 62.4 + - - +
132B TYR* 3.6 30.7 - - + -
134B LEU* 4.8 0.4 - - - -
155B PHE 3.7 1.4 - - - +
156B GLN* 3.2 24.9 - - - +
157B ALA 3.1 11.3 + - - +
159B PHE* 4.7 11.8 - - + -
172B CYS* 2.0 58.3 - - - -
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Residues in contact with SER 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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103B PRO* 3.4 1.4 - - - +
104B SER* 2.9 47.1 + - - +
106B THR* 5.1 3.1 + - - -
122B SER* 4.4 4.7 + - - -
123B CYS* 1.3 76.4 + - - +
125B SER* 1.3 65.2 + - - +
132B TYR* 3.7 1.3 - - - -
154B THR* 4.9 11.4 - - - -
155B PHE 3.6 4.7 - - - -
156B GLN* 3.6 24.8 + - - +
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Residues in contact with SER 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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101B GLU* 5.0 1.7 + - - +
102B LYS 4.8 3.3 + - - -
103B PRO* 4.2 9.5 - - - +
124B SER* 1.3 77.5 - - - +
126B GLN* 1.3 62.6 + - - +
127B SER* 3.0 27.5 + - - +
129B PHE* 3.5 17.1 - - - -
132B TYR* 3.2 15.0 - - - -
154B THR* 3.3 12.6 - - - +
155B PHE 2.9 30.3 + - - -
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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