Contacts of the strand formed by residues 182 - 191 (chain H) in PDB entry 1CBV
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 LEU 182 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122H ALA* 4.2 13.2 - - + -
123H LYS 4.7 1.1 - - - +
125H THR* 3.8 25.4 - - + +
152H GLY* 3.4 31.0 - - - +
153H TYR 3.4 10.3 - - - +
154H PHE* 3.9 18.4 - - + -
178H LEU* 4.6 0.7 - - - -
179H GLN* 2.5 45.6 + - - +
180H SER 3.6 2.4 - - - +
181H GLY* 1.3 85.4 - - - +
183H TYR* 1.3 62.1 + - - +
184H THR* 4.4 0.2 + - - -
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Residues in contact with TYR 183 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118H THR* 5.0 12.0 - - - +
152H GLY* 3.0 22.0 + - - -
153H TYR* 2.9 46.9 + + + +
154H PHE* 4.2 22.2 - + - -
155H PRO 4.7 0.7 - - - -
156H GLU* 4.1 32.4 + - + +
176H ALA* 4.2 12.8 - - + -
177H LEU* 3.1 23.1 - - - +
178H LEU* 3.5 29.3 - - + +
182H LEU* 1.3 73.2 - - - +
184H THR* 1.3 67.8 + - - +
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Residues in contact with THR 184 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149H LEU* 3.9 21.5 - - + -
150H VAL 3.4 13.2 - - - +
151H LYS* 3.9 23.9 - - + +
152H GLY* 4.0 0.7 + - - -
153H TYR* 4.6 1.1 - - - -
175H PRO 4.5 0.3 - - - +
176H ALA* 3.0 25.3 - - - -
177H LEU* 2.9 12.1 + - - +
179H GLN* 3.6 27.5 - - + +
182H LEU 4.1 0.4 + - - -
183H TYR* 1.3 77.3 + - - +
185H MET* 1.3 70.8 + - - +
165L LEU* 4.5 11.7 - - + -
183L THR* 5.6 4.9 - - + +
185L THR* 6.2 2.0 - - + -
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Residues in contact with MET 185 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149H LEU* 3.5 8.7 - - - +
150H VAL* 2.9 60.8 + - + +
153H TYR* 4.3 14.1 - - + +
158H VAL* 4.5 16.2 - - + +
160H VAL* 4.2 23.6 - - + -
173H THR* 5.0 9.2 - - + -
174H PHE 3.1 22.2 - - - +
175H PRO* 4.6 3.8 - - + -
176H ALA* 4.0 16.2 - - + +
184H THR* 1.3 79.4 - - - +
186H SER* 1.3 73.9 + - - +
187H SER* 5.4 0.2 - - - -
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Residues in contact with SER 186 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132H LEU* 5.5 0.2 - - - -
148H CYS 3.3 13.7 - - - -
149H LEU* 4.4 10.1 - - - -
150H VAL* 5.5 0.7 - - - -
160H VAL* 5.5 0.2 - - - +
174H PHE* 3.1 42.2 + - - +
185H MET* 1.3 86.7 - - - +
187H SER* 1.3 63.0 + - - +
138L VAL* 5.2 1.8 - - - -
140L PHE* 3.6 26.9 - - - -
181L SER* 3.9 8.1 - - - -
183L THR* 4.9 6.1 + - - -
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Residues in contact with SER 187 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147H GLY* 3.3 3.3 - - - -
148H CYS 3.1 30.3 + - - +
150H VAL* 6.2 0.4 - - - +
160H VAL* 3.7 30.0 - - - +
162H TRP* 2.7 34.4 + - - -
171H VAL* 3.6 6.1 - - - +
172H HIS 3.3 14.3 + - - -
173H THR* 4.5 1.5 + - - -
174H PHE* 4.3 0.7 - - - -
185H MET* 5.4 0.2 - - - -
186H SER* 1.3 77.6 - - - +
188H SER* 1.3 60.9 + - - +
140L PHE* 3.8 6.7 - - - -
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Residues in contact with SER 188 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145H THR* 3.9 8.5 - - - -
146H LEU 3.3 9.0 - - - -
147H GLY* 4.2 0.2 - - - -
162H TRP* 4.4 1.3 - - - -
170H SER 4.2 2.0 + - - -
171H VAL* 3.0 30.3 - - - +
172H HIS* 3.1 14.5 + - - +
174H PHE* 3.9 11.2 - - - -
187H SER* 1.3 74.0 + - - +
189H VAL* 1.3 61.2 - - - +
190H THR* 5.6 0.4 - - - -
140L PHE* 3.3 30.0 - - - -
142L ASN* 3.1 21.1 + - - -
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Residues in contact with VAL 189 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145H THR* 3.1 3.6 - - - +
146H LEU* 2.5 62.6 + - + +
162H TRP* 3.7 33.7 - - + -
164H SER* 4.1 9.2 - - - +
169H SER* 3.7 22.0 - - - +
170H SER 4.0 4.5 - - - -
171H VAL* 3.3 27.1 - - + -
188H SER* 1.3 74.8 - - - +
190H THR* 1.3 61.8 + - - +
191H VAL* 5.6 1.6 - - + -
201H VAL* 4.0 9.2 - - + -
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Residues in contact with THR 190 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143H SER* 3.4 32.5 - - - +
144H VAL* 3.4 12.8 - - - +
145H THR* 3.7 17.2 + - - +
167H LEU* 5.9 0.2 - - - +
168H SER 4.0 3.6 - - - +
169H SER* 3.1 27.9 + - - -
170H SER* 3.9 20.8 + - - +
188H SER* 5.6 0.3 - - - -
189H VAL* 1.3 78.7 + - - +
191H VAL* 1.3 60.6 + - - +
142L ASN* 5.4 3.3 + - - +
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Residues in contact with VAL 191 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143H SER* 2.9 9.7 - - - -
144H VAL* 2.6 55.6 + - + +
146H LEU* 3.8 26.0 - - + -
164H SER* 5.7 1.6 - - - -
167H LEU* 3.3 31.2 - - + -
189H VAL* 5.6 1.6 - - + -
190H THR* 1.3 73.6 - - - +
192H PRO* 1.3 87.4 - - + +
195H THR* 3.7 1.3 - - - +
196H TRP* 3.9 26.0 - - + -
201H VAL* 4.7 9.0 - - + -
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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