Contacts of the strand formed by residues 145 - 153 (chain B) in PDB entry 3RLQ
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 ALA 145 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B ILE* 5.2 0.9 - - - +
141B ALA 2.9 13.4 + - - +
142B TYR* 3.5 26.5 - - - +
143B LEU 3.8 0.2 - - - -
144B VAL* 1.3 80.5 - - + +
146B GLU* 1.3 61.1 + - - +
147B LYS 3.8 14.1 - - - +
148B VAL* 4.0 14.1 - - + -
188B LEU* 4.0 19.1 - - + -
189B HIS 3.4 11.9 - - - +
190B LEU* 4.1 0.7 - - - +
191B LYS* 3.8 6.6 - - - -
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Residues in contact with GLU 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ILE* 5.7 3.5 - - - +
87B ARG* 4.0 23.3 + - - -
142B TYR* 4.3 4.6 - - - -
145B ALA* 1.3 73.9 - - - +
147B LYS* 1.3 67.2 + - + +
165B SER* 3.5 26.2 - - - +
166B ALA* 5.5 0.2 - - - +
189B HIS* 3.0 20.1 + - + +
190B LEU 4.3 4.5 - - - +
191B LYS* 3.9 19.2 - - + +
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Residues in contact with LYS 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B TYR* 4.6 0.9 - - - -
145B ALA* 3.3 0.9 - - - +
146B GLU* 1.3 87.5 - - + +
148B VAL* 1.3 68.5 + - - +
163B GLU* 3.8 37.4 + - + +
164B SER 3.6 9.9 - - - +
165B SER* 3.4 21.3 - - - +
189B HIS* 2.9 68.3 + - + +
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Residues in contact with VAL 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B PHE* 3.9 30.1 - - + -
141B ALA* 3.9 9.4 - - + -
142B TYR* 3.5 33.7 - - + +
145B ALA* 4.0 7.0 - - + -
147B LYS* 1.3 79.0 - - - +
149B THR* 1.3 63.5 + - - +
150B VAL* 4.1 5.8 - - + -
162B TRP* 3.4 3.7 - - + -
163B GLU* 3.3 3.6 - - - +
164B SER 3.1 31.9 + - - +
186B VAL* 4.1 14.6 - - + -
187B ILE 3.4 6.7 - - - +
188B LEU* 3.8 18.6 - - + -
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Residues in contact with THR 149 (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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148B VAL* 1.3 74.4 - - - +
150B VAL* 1.3 64.5 + - - +
151B ILE* 3.9 24.2 - - + -
161B ALA* 4.9 4.0 - - + -
162B TRP 3.3 10.5 - - - +
163B GLU* 2.6 31.6 + - + +
185B LYS 3.6 1.0 - - - +
186B VAL* 3.6 1.4 - - - -
187B ILE* 2.7 57.3 + - + +
189B HIS* 3.7 14.3 + - - -
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Residues in contact with VAL 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B MET* 4.1 10.5 - - + -
103B LEU* 4.5 4.0 - - + -
107B LEU* 4.1 5.4 - - + -
138B PHE* 3.8 30.3 - - + -
148B VAL* 4.1 3.6 - - + -
149B THR* 1.3 76.7 - - - +
151B ILE* 1.3 63.4 + - - +
152B THR* 4.7 2.0 - - - +
160B TYR 3.7 1.0 - - - +
161B ALA* 3.5 1.9 - - - -
162B TRP* 2.7 60.2 + - + +
184B THR* 3.7 27.6 - - + -
185B LYS 3.3 2.7 - - - +
186B VAL* 4.3 7.2 - - + -
901B 3RQ 4.0 11.4 - - + -
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Residues in contact with ILE 151 (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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149B THR* 3.9 13.7 - - + -
150B VAL* 1.3 71.3 - - - +
152B THR* 1.3 65.4 + - - +
159B GLN* 3.6 15.0 - - + +
160B TYR 3.4 5.6 - - - +
161B ALA* 3.6 27.1 - - + -
175B ASP* 3.5 29.4 - - - +
180B MET* 3.7 12.2 - - - +
184B THR* 3.3 3.5 - - - +
185B LYS* 2.6 59.5 + - + +
187B ILE* 4.2 22.4 - - + -
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Residues in contact with THR 152 (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 MET* 3.0 53.8 + - + +
103B LEU* 4.0 27.4 - - + -
150B VAL* 4.7 1.3 - - - +
151B ILE* 1.3 78.4 - - - +
153B LYS* 1.3 60.1 + - - +
158B GLU 4.2 1.2 - - - +
159B GLN* 3.4 5.1 - - - -
160B TYR* 3.0 38.1 + - + +
180B MET* 4.5 1.3 - - - -
183B GLY 3.3 4.6 + - - -
184B THR* 2.8 22.9 + - - -
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Residues in contact with LYS 153 (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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72B SER* 6.1 0.4 - - - -
97B GLY* 3.7 6.5 - - - -
152B THR* 1.3 74.2 + - - +
154B HIS* 1.3 73.9 + - - +
155B ASN* 4.5 5.3 + - - +
156B ASP 4.5 2.4 - - - +
157B ASP 2.9 29.7 + - - +
158B GLU* 4.6 1.1 - - - +
159B GLN* 3.8 31.2 - - + +
180B MET* 3.5 30.5 - - + +
181B GLY 3.5 16.2 + - - +
182B ARG* 3.6 12.2 - - - +
183B GLY 2.8 36.3 + - - +
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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