Contacts of the strand formed by residues 166 - 176 (chain B) in PDB entry 3JRQ
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 TRP 166 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36B GLU* 2.8 32.5 + - + -
64B ARG* 3.7 25.4 - - + -
65B ILE 3.6 10.8 - - - +
66B HIS* 4.1 17.3 - + - +
67B ALA 3.8 4.7 - - - +
155B ARG* 3.8 3.1 - - - -
156B PHE* 2.9 57.6 + + + +
157B GLU 3.8 34.3 - - - -
164B ARG* 4.3 19.7 - - + -
165B ILE* 1.3 80.5 - - - +
167B THR* 1.3 81.7 + - - +
168B VAL* 3.9 1.6 - - - +
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Residues in contact with THR 167 (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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64B ARG* 3.4 2.6 - - - -
65B ILE* 2.6 42.7 + - - +
67B ALA 2.5 26.8 + - - -
68B PRO 3.4 0.7 + - - -
69B PRO* 3.2 18.1 - - + +
72B VAL* 3.9 13.9 - - + -
153B VAL* 3.4 33.4 - - + -
154B HIS 3.2 9.0 - - - +
166B TRP* 1.3 76.6 - - - +
168B VAL* 1.3 69.9 + - - +
169B VAL* 3.9 12.6 - - + -
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Residues in contact with VAL 168 (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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32B LEU* 4.0 14.8 - - + -
36B GLU* 3.7 28.5 - - + +
40B LEU* 3.8 22.0 - - + -
62B ALA* 4.6 1.8 - - + -
63B GLN 3.6 5.8 - - - +
64B ARG* 4.4 4.9 - - - -
153B VAL* 3.7 0.5 - - - -
154B HIS* 2.8 37.5 + - + +
156B PHE* 3.5 31.1 - - + -
166B TRP* 3.9 2.5 - - + +
167B THR* 1.3 79.2 - - - +
169B VAL* 1.3 72.9 + - - +
170B LEU* 4.2 8.3 - - + -
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Residues in contact with VAL 169 (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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62B ALA* 3.3 4.0 - - - -
63B GLN* 2.8 38.2 + - + +
65B ILE* 3.7 17.3 - - + -
72B VAL* 3.5 32.5 - - + -
151B THR* 3.8 21.3 - - + -
152B THR 3.4 9.6 - - - +
153B VAL* 4.4 6.5 - - + -
167B THR* 3.9 6.1 - - + -
168B VAL* 1.3 78.4 - - - +
170B LEU* 1.3 65.7 + - - +
198B LEU* 3.9 24.8 - - + +
201B LEU* 4.3 5.8 - - + -
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Residues in contact with LEU 170 (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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32B LEU* 4.7 3.1 - - + -
40B LEU* 4.0 22.2 - - + +
43B SER* 4.9 0.9 - - - -
44B ILE* 4.1 20.2 - - + -
48B HIS* 3.5 12.0 - - + +
60B LEU* 4.2 18.2 - - + -
61B LEU 3.2 5.4 - - - +
62B ALA* 3.7 26.2 - - + -
151B THR* 3.3 4.9 - - - +
152B THR* 2.9 38.3 + - - +
154B HIS* 3.3 30.7 - - + +
168B VAL* 4.2 9.8 + - + -
169B VAL* 1.3 76.5 - - - +
171B GLU* 1.3 60.2 + - - +
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Residues in contact with GLU 171 (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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1B A8S 3.0 24.3 - - - +
48B HIS* 4.3 0.4 - - - -
60B LEU* 3.5 1.4 - - - -
61B LEU* 2.8 35.3 + - - +
85B TYR* 4.9 8.5 + - - -
86B LYS* 5.6 1.6 - - - -
135B PHE* 4.9 2.4 - - - -
147B TYR* 3.7 7.6 + - - -
149B SER* 2.9 23.5 + - - +
150B VAL 3.2 8.3 - - - +
151B THR* 3.8 17.8 + - + +
169B VAL 4.4 0.2 + - - -
170B LEU* 1.3 75.9 - - - +
172B SER* 1.3 67.8 + - - +
194B ILE* 3.6 31.6 - - + +
197B ASN* 5.4 4.9 + - - +
198B LEU* 4.3 18.6 - - + +
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Residues in contact with SER 172 (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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48B HIS* 2.6 42.4 + - - +
50B TYR* 2.7 26.7 + - - -
59B SER 3.1 16.2 - - - -
60B LEU* 3.9 6.7 - - - -
149B SER* 3.1 7.7 + - - -
150B VAL 2.9 25.4 + - - -
171B GLU* 1.3 77.7 - - - +
173B TYR* 1.3 65.1 + - - +
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Residues in contact with TYR 173 (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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50B TYR* 3.6 8.0 - - - -
57B CYS* 4.3 5.4 - - - -
58B SER* 3.0 26.2 + - - -
59B SER* 3.2 44.1 + - - -
61B LEU* 4.3 2.2 - - + -
147B TYR* 3.4 34.1 - + + +
148B LYS 3.0 13.9 - - - +
172B SER* 1.3 78.8 - - - +
174B VAL* 1.3 69.2 + - - +
175B VAL* 4.0 15.5 - - + -
187B ARG* 3.4 21.0 - - - +
190B ALA* 3.5 16.9 - - + +
191B ASP* 2.7 23.7 + - - -
194B ILE* 3.4 27.6 - - + -
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Residues in contact with VAL 174 (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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50B TYR* 3.2 45.3 - - + -
51B GLN 4.3 8.7 - - - +
52B LEU* 5.8 0.4 - - + -
56B ARG* 3.7 38.4 - - + +
57B CYS 3.1 15.9 - - - +
58B SER* 4.2 4.3 - - - +
146B ASN 3.4 1.1 - - - +
147B TYR* 3.4 1.0 - - - -
148B LYS* 2.9 44.7 + - + +
173B TYR* 1.3 75.5 - - - +
175B VAL* 1.3 68.4 + - - +
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Residues in contact with VAL 175 (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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56B ARG* 3.4 13.4 - - - +
57B CYS* 2.7 39.6 + - + +
144B LEU* 3.8 20.4 - - + -
145B ARG 3.4 14.4 - - - +
146B ASN 3.9 2.0 - - - -
147B TYR* 3.7 29.6 - - + -
173B TYR* 4.0 13.5 - - + -
174B VAL* 1.3 77.7 - - - +
176B ASP* 1.4 66.5 + - - +
186B THR* 3.6 30.1 - - + -
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Residues in contact with ASP 176 (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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55B GLY 3.3 9.0 - - - +
56B ARG* 3.1 28.9 + - - +
143B ARG 4.7 4.3 - - - +
144B LEU* 5.1 0.2 - - - -
145B ARG* 3.3 27.4 + - + +
146B ASN* 3.1 21.8 - - - +
175B VAL* 1.4 89.3 - - - +
177B VAL* 1.3 66.9 + - - +
178B PRO* 3.3 10.3 - - + +
186B THR* 4.4 0.5 - - - +
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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