Contacts of the strand formed by residues 113 - 122 (chain B) in PDB entry 2G5T
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 113 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B ILE* 3.5 9.7 - - - +
108B SER* 3.0 29.4 + - - +
112B GLN* 1.3 103.3 - - + +
114B ILE* 1.3 64.7 + - - +
134B ILE* 3.9 11.9 - - + -
135B TYR 3.5 2.5 - - - -
136B ASP* 3.2 46.0 - - + -
137B LEU* 4.0 0.7 - - - -
138B ASN* 5.3 2.0 - - - -
143B ILE* 4.1 4.9 - - + -
157B TRP* 3.5 20.0 - - + -
162B HIS* 3.8 24.7 - + + -
177B GLU* 5.4 1.8 - - - -
178B PRO* 3.8 38.8 - - + -
179B ASN* 4.9 5.2 - - - -
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Residues in contact with ILE 114 (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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76B ILE* 5.9 0.4 - - + -
89B PHE* 4.8 0.4 - - + -
90B LEU* 4.1 19.3 - - + -
95B PHE* 4.5 8.3 - - + -
105B TYR* 4.2 15.0 - - + -
106B SER 3.7 3.1 - - - +
107B ILE* 3.8 22.0 - - + -
113B PHE* 1.3 80.5 - - - +
115B LEU* 1.3 70.5 + - - +
116B LEU* 3.7 14.9 + - + +
134B ILE* 3.4 5.7 - - - +
135B TYR* 3.1 43.2 + - + +
137B LEU* 3.2 40.4 - - + -
157B TRP* 4.3 3.6 - - - -
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Residues in contact with LEU 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B TYR* 3.2 8.3 - - - -
106B SER* 2.7 58.4 + - - +
114B ILE* 1.3 73.4 - - - +
116B LEU* 1.3 61.0 + - - +
117B GLU* 3.9 1.3 + - + +
132B TYR* 3.8 24.2 - - + -
133B ASP 3.9 0.2 - - - -
134B ILE* 4.0 24.0 - - + -
148B ILE* 4.0 18.4 - - + -
155B VAL* 3.7 34.3 - - + +
156B THR* 5.5 0.7 - - - -
157B TRP* 3.8 14.5 - - + +
164B LEU* 4.5 7.4 - - + -
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Residues in contact with LEU 116 (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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95B PHE* 3.6 43.1 - - + -
98B PHE* 4.1 22.0 - - + -
102B ILE* 4.3 12.1 - - + -
104B ASP 4.1 1.6 - - - -
105B TYR* 3.6 31.4 - - + -
114B ILE* 4.1 11.7 - - + +
115B LEU* 1.3 74.5 - - - +
117B GLU* 1.3 59.9 + - - +
118B TYR* 3.9 2.7 - - + -
131B SER 3.5 0.7 - - - +
132B TYR* 3.2 12.4 - - - -
133B ASP* 2.8 42.4 + - + +
135B TYR* 4.5 2.2 - - + -
142B LEU* 4.1 18.2 - - + -
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Residues in contact with GLU 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B ILE* 3.7 3.4 - - - +
103B ASN* 2.7 57.1 + - - +
104B ASP* 3.0 31.9 + - + +
115B LEU* 3.9 1.7 + - + +
116B LEU* 1.3 73.0 - - - +
118B TYR* 1.3 59.1 + - - +
120B TYR* 4.3 0.7 - - - -
128B TYR* 2.7 40.7 + - - -
130B ALA* 3.8 11.9 - - + -
131B SER 3.6 3.1 - - - -
132B TYR* 3.3 28.2 + - + -
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Residues in contact with TYR 118 (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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98B PHE* 3.8 15.9 - + + -
100B HIS* 3.5 42.6 + + + -
101B SER 3.1 24.0 - - - +
102B ILE* 4.4 2.0 - - + -
103B ASN* 3.2 7.6 - - - -
116B LEU 3.9 5.8 - - - -
117B GLU* 1.3 75.3 - - - +
119B ASN* 1.3 104.9 + - - +
120B TYR 3.2 3.2 + - - -
130B ALA* 3.3 2.6 - - - +
131B SER* 2.8 57.8 + - - -
132B TYR 4.0 4.0 + - - -
133B ASP* 2.6 31.4 + - - -
150B ASN* 4.6 3.8 + - - -
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Residues in contact with ASN 119 (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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100B HIS* 4.5 12.9 + - - +
101B SER 4.4 2.6 + - - -
103B ASN* 4.3 0.2 + - - -
118B TYR* 1.3 109.4 - - - +
120B TYR* 1.3 63.6 + - - +
121B VAL* 3.4 15.1 + - + +
130B ALA* 3.5 9.9 - - - -
131B SER* 3.4 17.2 + - - +
150B ASN* 5.3 0.4 + - - -
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Residues in contact with TYR 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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103B ASN* 3.5 36.8 - - + +
117B GLU* 4.3 0.9 - - - +
118B TYR 3.2 3.0 - - - -
119B ASN* 1.3 75.2 - - - +
121B VAL* 1.3 60.7 + - - +
122B LYS* 3.2 40.2 + - + +
127B SER 5.1 0.2 + - - -
128B TYR* 3.3 49.9 - + + +
129B THR 3.8 3.4 - - - -
130B ALA* 4.2 2.7 - - - -
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Residues in contact with VAL 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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119B ASN* 3.5 15.7 - - + +
120B TYR* 1.3 74.8 - - - +
122B LYS* 1.3 70.6 + - - +
123B GLN* 4.6 0.9 - - - +
128B TYR* 3.3 3.5 - - - +
129B THR* 2.8 49.3 + - - +
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Residues in contact with LYS 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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120B TYR* 3.2 32.8 + - + +
121B VAL* 1.3 80.7 - - - +
123B GLN* 1.3 86.6 + - - +
124B TRP* 3.1 20.9 + - - +
125B ARG* 4.8 7.1 - - - +
127B SER 4.4 1.3 - - - +
128B TYR* 3.7 9.4 - - - -
709B ASP* 5.8 0.2 + - - -
739B ASP* 3.0 25.8 + - - -
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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