Contacts of the strand formed by residues 118 - 124 (chain B) in PDB entry 5T5W
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 ILE 118 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128A HIS* 3.4 29.6 - - + +
175A PHE* 3.8 19.3 - - + -
177A VAL* 4.3 3.8 - - + -
179A ARG* 4.3 18.4 - - - +
114B GLN* 3.5 3.3 - - - +
115B THR* 2.7 48.0 + - + +
116B GLU 3.5 0.4 + - - -
117B GLU* 1.3 81.8 - - - +
119B LEU* 1.3 65.8 + - - +
120B SER* 4.1 3.7 + - - +
163B GLN* 3.9 37.2 - - + +
164B ILE 3.5 7.6 - - - +
165B THR* 4.3 0.2 - - - -
166B LEU* 4.3 3.3 - - - +
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Residues in contact with LEU 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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112B LEU* 4.5 11.4 - - + -
113B THR 3.2 26.5 - - - +
114B GLN* 4.5 7.2 - - + +
118B ILE* 1.3 73.8 - - - +
120B SER* 1.3 66.1 + - - +
142B PHE* 4.2 14.6 - - + -
162B VAL 3.3 3.1 - - - +
164B ILE* 2.7 49.4 + - + +
166B LEU* 3.7 25.7 - - + +
176B LEU* 3.7 17.5 - - + -
198B PHE* 3.7 33.9 - - + -
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Residues in contact with SER 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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111B VAL 3.5 4.5 + - - +
112B LEU* 3.6 2.3 - - - -
113B THR* 2.6 54.9 + - - +
118B ILE* 4.1 4.1 - - - -
119B LEU* 1.3 75.6 - - - +
121B ALA* 1.3 60.0 + - - +
122B ASN* 3.9 1.4 - - - +
161B PRO* 4.1 19.0 - - - +
162B VAL 3.2 7.6 - - - -
163B GLN* 4.4 12.6 - - - +
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Residues in contact with ALA 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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110B LEU* 4.1 15.5 - - + -
112B LEU* 3.7 23.3 - - + -
119B LEU 4.0 0.4 + - - -
120B SER* 1.3 71.0 - - - +
122B ASN* 1.3 60.3 + - - +
138B TYR* 3.3 12.8 + - - -
140B VAL* 4.4 14.8 - - + -
161B PRO* 4.4 0.4 - - - -
162B VAL* 2.9 30.7 + - + +
164B ILE* 4.7 4.5 - - + -
176B LEU* 4.2 13.0 - - + -
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Residues in contact with ASN 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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109B VAL 3.5 0.3 - - - +
110B LEU* 3.2 4.2 - - - -
111B VAL* 2.7 52.2 + - + +
120B SER* 3.9 1.3 - - - +
121B ALA* 1.3 72.7 - - - +
123B ALA* 1.3 66.2 + - - +
124B THR* 4.7 4.4 - - - +
138B TYR* 4.0 1.1 - - - -
159B GLY* 4.3 0.7 + - - -
160B GLN 3.6 6.8 + - - +
161B PRO* 3.6 21.4 - - + -
301B NAG 1.4 70.4 + - + +
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Residues in contact with ALA 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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108B PRO* 3.6 23.1 - - + -
109B VAL 3.6 4.0 - - - -
110B LEU* 4.0 3.8 - - + -
122B ASN* 1.3 78.0 + - - +
124B THR* 1.3 59.8 + - - +
125B TYR* 4.1 6.3 - - + -
138B TYR* 3.6 43.7 + - + -
158B HIS* 3.7 8.4 - - + -
159B GLY 4.9 0.5 + - - -
301B NAG 3.2 24.6 - - - +
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Residues in contact with THR 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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108B PRO* 3.7 2.6 - - - +
109B VAL* 2.6 60.7 + - - +
111B VAL* 3.6 27.4 - - + +
122B ASN* 4.5 2.0 - - - +
123B ALA* 1.3 78.4 - - - +
125B TYR* 1.3 70.5 + - - +
301B NAG 4.0 18.4 - - - +
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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