Contacts of the strand formed by residues 166 - 177 (chain B) in PDB entry 1R74
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 VAL 166 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131B GLY* 5.1 0.7 - - - -
132B PHE 3.8 4.3 - - - +
135B VAL* 3.6 26.2 - - + -
162B ILE 4.0 5.8 - - - +
163B ALA* 2.9 16.7 + - - +
164B SER 3.2 4.2 - - - +
165B MET* 1.4 75.9 - - - +
167B ARG* 1.3 69.1 + - - +
170B GLY* 3.6 26.0 - - - +
171B LEU 3.9 11.0 - - - +
172B LEU* 4.1 15.5 - - + +
260B PHE* 4.2 8.5 - - + -
292B ARG* 2.8 37.7 + - + +
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Residues in contact with ARG 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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55B HIS 5.6 3.4 + - - -
56B GLY 5.9 0.8 + - - -
130B GLY 4.8 2.5 - - - +
131B GLY* 3.4 26.5 - - - +
132B PHE 2.9 37.4 + - - +
133B ASP* 3.0 32.8 + - - +
165B MET 3.7 2.2 + - - -
166B VAL* 1.3 79.3 - - - +
168B ALA* 1.3 75.2 + - - +
169B GLY* 3.2 11.2 + - - -
170B GLY* 2.8 31.9 + - - +
292B ARG* 3.6 2.9 - - - +
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Residues in contact with ALA 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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167B ARG* 1.3 94.0 + - - +
169B GLY* 1.3 58.3 + - - +
170B GLY 3.2 2.1 + - - -
292B ARG* 3.7 15.8 - - - +
293B THR 5.7 4.5 - - - +
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Residues in contact with GLY 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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55B HIS* 5.8 0.5 - - - -
167B ARG* 3.2 8.6 + - - -
168B ALA* 1.3 70.0 - - - +
170B GLY* 1.3 61.3 + - - +
171B LEU* 5.2 1.2 - - - +
291B LYS* 3.4 21.7 - - - +
292B ARG 3.2 23.6 + - - -
293B THR* 4.9 2.0 - - - +
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Residues in contact with GLY 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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57B CYS* 6.2 0.2 - - - -
133B ASP 3.2 15.5 - - - -
166B VAL* 3.6 8.9 - - - +
167B ARG* 2.8 31.0 + - - -
168B ALA 3.2 2.0 + - - -
169B GLY* 1.3 71.8 - - - +
171B LEU* 1.3 62.7 + - - -
291B LYS* 3.1 23.7 - - - -
292B ARG 3.1 6.3 + - - -
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Residues in contact with LEU 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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51B LEU* 4.0 29.8 - - + +
52B LEU* 5.0 1.3 - - + -
55B HIS* 3.1 51.4 - - + +
57B CYS* 4.1 14.6 - - - -
133B ASP 2.9 8.9 + - - -
134B ALA* 3.1 9.5 - - + -
135B VAL 2.9 25.5 + - - -
166B VAL* 3.9 10.5 - - - +
169B GLY 5.2 0.7 - - - +
170B GLY* 1.3 75.1 - - - +
172B LEU* 1.3 59.3 + - - +
173B VAL* 4.4 8.7 - - + -
289B VAL* 4.4 10.1 - - + -
290B LEU 3.0 9.2 - - - +
291B LYS* 3.8 21.8 - - + -
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Residues in contact with LEU 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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135B VAL* 3.4 24.9 - - + +
136B ILE* 5.2 0.7 - - - -
137B CYS 5.2 1.3 - - - +
159B LEU* 5.7 1.3 - - + +
162B ILE* 3.5 34.3 - - + -
163B ALA 5.1 2.5 - - - +
166B VAL* 4.1 11.6 - - + +
171B LEU* 1.3 73.7 - - - +
173B VAL* 1.3 66.0 + - - +
174B ILE* 4.0 28.0 - - + -
256B LEU* 4.1 17.9 - - + -
260B PHE* 4.1 24.5 - - + -
288B HIS 3.4 4.2 - - - +
289B VAL* 3.5 2.4 - - - +
290B LEU* 2.7 37.9 + - + +
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Residues in contact with VAL 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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47B TRP* 3.9 24.5 - - + -
48B LEU* 5.2 2.0 - - + -
51B LEU* 3.8 24.0 - - + -
52B LEU* 5.3 2.5 - - + -
134B ALA* 5.2 2.9 - - + -
135B VAL 2.9 14.1 + - - +
136B ILE* 3.4 15.3 - - + -
137B CYS 2.7 32.4 + - - -
138B LEU* 3.4 20.2 - - + +
171B LEU* 4.4 14.4 - - + -
172B LEU* 1.3 76.7 - - - +
174B ILE* 1.3 58.2 + - - +
287B ILE* 4.0 9.6 - - + -
288B HIS 3.5 4.3 - - - +
289B VAL* 4.6 4.9 - - + -
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Residues in contact with ILE 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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137B CYS* 3.2 29.8 - - + +
138B LEU* 3.8 0.9 - - - +
142B PHE* 4.2 12.6 - - + -
159B LEU* 4.1 18.2 - - + -
162B ILE* 4.8 4.9 - - + -
172B LEU* 4.0 24.5 - - + -
173B VAL* 1.3 80.1 - - - +
175B ASP* 1.3 68.3 + - - +
252B PHE* 4.1 20.9 - - + -
256B LEU* 3.9 15.9 - - + -
287B ILE* 4.6 0.2 - - - -
288B HIS* 2.9 46.5 + - + +
290B LEU* 5.0 0.4 - - + -
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Residues in contact with ASP 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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137B CYS 3.3 3.9 + - - +
138B LEU* 3.3 12.2 - - + -
139B GLY 2.8 22.0 + - - -
140B ASN* 2.9 26.1 + - - +
141B SER 4.4 0.3 + - - -
142B PHE* 4.6 10.4 + - - +
174B ILE* 1.3 82.2 - - - +
176B HIS* 1.3 69.8 - - - +
195B TYR* 2.6 32.9 + - - +
252B PHE* 4.8 1.8 - - - -
285B TYR* 4.0 5.2 - - + -
286B PHE 3.1 13.5 - - - +
287B ILE* 3.9 10.3 - - + -
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Residues in contact with HIS 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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140B ASN* 3.3 13.2 - - - +
142B PHE* 6.3 0.2 - - + -
143B ALA* 5.2 4.3 - - + +
175B ASP* 1.3 77.5 - - - +
177B ARG* 1.3 84.0 + - - +
178B ASN* 5.0 0.4 - - - -
179B TYR* 4.6 6.3 - - + -
247B HIS* 4.0 22.5 + - + -
249B LEU* 4.1 10.2 - - + +
252B PHE* 3.8 29.4 - + + +
285B TYR* 3.6 6.4 - - - -
286B PHE* 2.9 64.7 + + + +
288B HIS* 3.5 32.1 - + - -
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Residues in contact with ARG 177 (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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140B ASN* 3.1 16.9 + - - +
176B HIS* 1.3 96.4 + - - +
178B ASN* 1.4 55.7 + - - +
179B TYR* 2.8 32.3 + - + -
182B ILE* 3.8 14.1 - - + +
188B ALA* 3.3 33.7 + - - +
189B PRO* 2.7 39.5 + - - +
190B PRO* 5.9 0.4 - - - +
192B LYS* 4.0 15.8 - - - +
220B LEU* 4.4 8.1 - - - +
222B TYR* 4.9 1.6 + - - -
284B CYS* 3.5 18.9 + - - +
285B TYR* 3.7 24.3 - - + -
2001B CIT 4.2 32.9 + - - -
2284B BME 5.7 1.8 - - - -
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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