Contacts of the strand formed by residues 134 - 142 (chain G) in PDB entry 2Q5E
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 THR 134 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211F ARG* 5.0 3.0 + - - +
130G GLU* 4.2 0.7 - - - -
131G ILE 3.0 23.8 + - - +
132G GLU 3.1 13.9 + - - +
133G GLY* 1.3 78.7 - - - +
135G THR* 1.3 65.8 + - - +
136G HIS* 3.4 24.9 + - - -
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Residues in contact with THR 135 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128G PRO* 4.5 10.4 - - - +
129G ILE 3.0 16.8 - - - -
130G GLU* 3.9 14.1 - - + +
133G GLY 4.8 3.6 - - - +
134G THR* 1.3 80.0 + - - +
136G HIS* 1.3 71.8 + - - +
137G GLN* 4.9 4.0 + - - +
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Residues in contact with HIS 136 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211F ARG* 3.5 47.1 + - - -
117G PHE* 4.4 20.9 - + + -
128G PRO* 3.3 4.3 - - - +
129G ILE* 2.6 36.3 + - + +
131G ILE* 3.3 49.2 + - + +
134G THR* 3.4 28.8 + - - -
135G THR* 1.3 77.3 + - - +
137G GLN* 1.3 65.3 + - - +
138G VAL* 5.1 0.2 - - - -
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Residues in contact with GLN 137 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117G PHE* 3.9 19.2 - - - +
126G ILE* 3.0 35.0 + - + +
127G VAL 3.5 2.5 - - - -
128G PRO* 3.3 29.6 - - - +
135G THR* 4.9 4.0 + - - +
136G HIS* 1.3 76.9 - - - +
138G VAL* 1.3 63.5 + - - +
139G TYR* 4.0 30.3 + - + +
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Residues in contact with VAL 138 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115G SER* 3.3 35.9 - - - +
116G SER 3.6 10.3 - - - +
117G PHE* 4.1 19.3 - - + -
126G ILE* 3.3 5.2 - - - -
127G VAL* 2.5 46.5 + - + +
129G ILE* 3.5 34.8 - - + -
136G HIS 4.9 0.4 - - - +
137G GLN* 1.3 77.6 - - - +
139G TYR* 1.3 60.8 + - - +
140G VAL* 3.5 11.6 + - + +
169G TYR* 4.1 11.7 - - + -
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Residues in contact with TYR 139 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114G HIS 3.7 2.9 - - - +
115G SER* 3.5 2.3 - - - -
116G SER* 2.9 35.3 + - - +
117G PHE 4.2 1.8 - - - -
118G LYS 3.4 20.2 - - - +
119G PRO* 3.3 40.2 - - + +
120G ILE* 3.4 36.2 - - + +
123G ALA* 4.4 8.5 - - + -
125G PHE 3.9 2.5 - - - -
126G ILE* 3.5 41.6 - - + +
137G GLN* 4.0 28.0 + - + +
138G VAL* 1.3 70.3 - - - +
140G VAL* 1.3 62.5 + - - +
141G LEU* 4.8 0.2 - - - +
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Residues in contact with VAL 140 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113G VAL* 4.0 22.7 - - + -
114G HIS 3.8 3.1 - - - -
115G SER* 3.6 21.8 - - - +
124G ASP* 3.1 24.9 + - - +
125G PHE* 3.1 39.4 + - + +
127G VAL* 3.8 20.9 - - + -
138G VAL* 3.5 20.9 - - + +
139G TYR* 1.3 75.1 - - - +
141G LEU* 1.3 63.8 + - - +
173G VAL* 4.3 12.8 - - + -
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Residues in contact with LEU 141 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113G VAL* 3.4 4.9 - - - -
114G HIS* 3.2 30.0 + - + +
120G ILE* 3.5 26.9 - - + -
123G ALA* 3.4 38.6 - - - +
124G ASP* 3.4 8.1 - - - +
139G TYR 4.8 0.7 - - - +
140G VAL* 1.3 76.5 - - - +
142G LYS* 1.3 60.2 + - - +
236G TRP* 3.0 30.2 - - + -
237G PHE 4.5 12.6 - - - +
238G ASP* 4.6 14.6 - - + -
240G MET* 5.6 9.6 - - + -
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Residues in contact with LYS 142 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112G LEU 4.1 4.5 - - - -
113G VAL* 4.5 2.7 - - - -
124G ASP* 3.0 23.6 + - + +
125G PHE* 3.4 40.2 - - + -
140G VAL 4.3 0.2 - - - -
141G LEU* 1.3 70.5 - - - +
143G ARG* 1.3 65.7 + - - +
144G PRO* 3.6 2.4 - - - +
146G VAL* 3.7 19.1 - - + -
147G ASP* 2.9 30.9 + - - +
177G LEU* 4.0 12.1 - - + -
179G ARG* 5.2 4.2 - - - +
236G TRP* 3.2 11.8 - - - -
240G MET* 4.7 6.1 - - - +
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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