Contacts of the strand formed by residues 171 - 178 (chain B) in PDB entry 4CQM
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 171 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B MET* 3.8 26.5 - - + -
122B MET* 3.7 31.2 - - + +
123B ILE* 3.7 28.7 - - + -
128B GLY 3.2 21.8 - - - +
130B ILE* 4.6 1.6 - - + -
163B ALA 4.6 0.9 - - - +
166B VAL* 3.3 41.0 + - + +
167B ALA* 3.9 7.7 + - - +
169B LYS* 3.1 15.4 - - + +
170B LYS* 1.3 79.7 - - - +
172B ARG* 1.3 70.0 + - - +
173B VAL* 4.2 3.8 + - + +
223B THR* 4.3 3.8 + - - +
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Residues in contact with ARG 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A MET* 3.6 16.8 - - + -
128B GLY 3.0 9.8 + - - +
129B SER* 3.0 17.2 + - - +
130B ILE* 2.6 35.6 + - - +
170B LYS 5.0 3.6 - - - +
171B ILE* 1.3 79.2 - - - +
173B VAL* 1.3 57.4 + - - +
174B ASN* 3.8 4.1 - - - +
216B LEU 2.6 22.6 + - - -
217B LEU 2.7 31.1 + - - -
218B GLU 3.8 1.2 - - - +
219B SER 2.7 24.0 + - - -
220B PRO* 3.2 30.1 + - - +
222B ILE 2.9 26.7 + - - +
223B THR* 3.5 4.7 - - - +
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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
----------------------------------------------------------
119B MET* 4.3 9.0 - - + -
130B ILE* 3.3 19.3 - - + +
132B ASN* 4.1 11.9 - - - +
159B SER* 3.6 40.1 - - - +
162B LEU* 3.9 31.9 - - + -
163B ALA* 3.8 11.0 - - + +
166B VAL* 4.4 5.2 - - + -
171B ILE* 4.2 1.3 + - + -
172B ARG* 1.3 77.0 - - - +
174B ASN* 1.3 60.3 + - - +
223B THR* 3.2 6.9 + - - -
224B GLY* 2.7 34.8 + - - -
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Residues in contact with ASN 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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129B SER* 5.6 0.4 + - - -
130B ILE 2.8 11.7 + - - +
131B VAL* 3.3 5.6 - - + +
132B ASN* 2.9 24.8 + - - +
159B SER* 4.5 2.6 + - - -
172B ARG* 3.8 12.5 - - - +
173B VAL* 1.3 79.9 - - - +
175B VAL* 1.3 68.3 + - - +
216B LEU* 3.7 25.1 + - + +
222B ILE* 2.9 32.6 + - - +
223B THR* 3.3 8.7 - - - +
224B GLY* 3.2 4.1 + - - -
225B HIS* 2.8 40.5 + - - +
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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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132B ASN* 3.3 15.7 - - + +
134B GLY* 4.1 11.9 - - - +
152B LYS 6.1 0.2 - - - +
155B LEU* 3.6 16.4 - - + +
156B VAL* 4.5 11.7 - - + -
159B SER* 3.2 32.8 - - - +
160B ARG* 6.5 0.2 - - + -
174B ASN* 1.3 76.9 - - - +
176B VAL* 1.3 68.5 + - - +
177B ALA* 4.5 1.8 - - + +
216B LEU* 4.1 1.1 - - - +
225B HIS 3.0 8.2 + - - +
226B VAL* 3.2 27.4 - - + -
227B LEU* 2.7 32.9 + - - +
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Residues in contact with VAL 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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131B VAL* 3.6 23.3 - - + +
132B ASN 3.0 7.3 + - - +
133B VAL* 3.8 5.2 - - + -
134B GLY* 2.9 26.0 + - - -
175B VAL* 1.3 71.7 - - - +
177B ALA* 1.3 62.9 + - - +
178B PRO* 3.1 7.5 - - + +
209B VAL* 3.8 29.2 - - + -
212B ALA* 3.7 18.4 - - + +
213B VAL* 3.9 11.2 - - + -
216B LEU* 3.7 18.8 - - + -
227B LEU* 3.5 4.9 - - + +
229B VAL* 3.9 18.2 - - + -
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Residues in contact with ALA 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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135B SER 3.9 23.6 - - - +
136B ILE* 4.1 6.4 + - + +
139B LEU* 5.4 2.5 - - + -
175B VAL* 3.9 2.6 + - + -
176B VAL* 1.3 72.9 - - - +
178B PRO* 1.3 66.3 - - - +
226B VAL* 3.8 22.0 - - + -
227B LEU 2.6 14.3 + - - +
228B VAL* 3.4 15.0 - - + +
229B VAL 2.9 21.3 + - - -
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Residues in contact with PRO 178 (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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14B ILE* 4.3 18.4 - - + -
133B VAL* 4.4 5.2 - - + -
134B GLY 3.3 19.3 - - - +
135B SER* 3.6 5.6 + - - -
136B ILE* 3.0 23.0 + - - -
176B VAL* 3.1 18.8 - - + +
177B ALA* 1.3 85.1 - - - +
179B GLY* 1.3 66.1 + - - +
181B VAL* 5.5 5.2 - - + -
209B VAL* 4.1 26.9 - - + -
229B VAL* 3.2 11.9 - - + +
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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