Contacts of the strand formed by residues 166 - 174 (chain H) in PDB entry 2X5V
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 GLY 166 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156H PRO* 3.5 6.6 - - - +
157H VAL* 3.5 21.3 + - - +
164H GLU* 3.5 15.4 + - - +
165H ALA* 1.3 79.7 - - - +
167H THR* 1.3 66.4 + - - -
185H LEU* 4.8 4.3 - - - -
186H SER 3.1 13.7 - - - -
188H ALA* 4.2 12.1 - - - +
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Residues in contact with THR 167 (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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154H GLY* 3.4 20.9 - - - +
155H LEU 3.2 19.7 - - - +
156H PRO* 4.3 2.5 - - + -
157H VAL 4.4 0.2 - - - +
164H GLU* 4.7 4.3 + - - -
166H GLY* 1.3 77.6 + - - -
168H VAL* 1.3 74.9 - - - +
185H LEU* 3.9 5.2 - - - +
186H SER* 3.0 39.2 + - - -
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Residues in contact with VAL 168 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152H PRO* 3.3 35.7 - - + +
153H ARG* 3.7 11.2 - - - +
154H GLY* 3.0 19.3 + - - -
155H LEU 3.0 12.4 + - - +
157H VAL* 3.5 25.4 - - + +
167H THR* 1.3 80.2 - - - +
169H THR* 1.3 61.8 + - - +
170H ASP 3.9 13.5 - - - +
171H LEU* 4.4 4.0 - - + -
183H LEU* 4.7 13.5 - - + -
184H GLU 3.5 13.0 - - - +
185H LEU* 4.0 2.9 - - + +
208H ILE* 4.0 15.0 - - + -
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Residues in contact with THR 169 (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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138H ARG* 5.1 2.3 + - - +
153H ARG* 4.3 10.6 - - - +
154H GLY 5.0 0.9 - - - +
167H THR* 4.2 4.0 - - - -
168H VAL* 1.3 75.5 - - - +
170H ASP* 1.3 65.6 + - + +
184H GLU* 2.8 42.0 + - + +
186H SER* 4.1 18.2 - - - +
193H THR* 4.3 10.5 - - + -
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Residues in contact with ASP 170 (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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136H PRO* 3.3 4.5 - - + +
137H LEU* 3.7 15.8 - - - +
138H ARG* 2.9 59.4 + - - +
153H ARG* 3.8 18.2 + - - -
168H VAL* 3.9 4.7 - - - +
169H THR* 1.3 79.6 - - + +
171H LEU* 1.3 81.9 + - - +
183H LEU* 3.9 1.2 - - - -
184H GLU* 3.0 38.1 + - - +
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Residues in contact with LEU 171 (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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136H PRO* 3.2 4.9 - - - +
137H LEU* 2.9 32.2 + - + +
145H ILE* 3.6 26.5 - - + -
152H PRO* 3.6 24.5 - - + -
153H ARG* 3.3 31.6 - - + +
168H VAL* 4.4 1.3 - - + -
170H ASP* 1.3 81.3 + - - +
172H TRP* 1.3 64.8 + - - +
173H VAL 4.0 0.9 - - - -
180H PHE* 3.4 38.1 - - + -
182H TYR 3.9 4.7 - - - +
183H LEU* 3.8 13.9 - - + -
10M ILE* 4.3 8.7 - - + -
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Residues in contact with TRP 172 (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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134H ILE* 4.0 18.3 - - + +
135H VAL* 3.3 11.4 - - - +
136H PRO* 3.6 37.2 - - + +
170H ASP* 4.7 0.2 - - - +
171H LEU* 1.3 82.9 - - - +
173H VAL* 1.3 62.9 + - - +
174H ASP 3.9 0.2 + - - -
180H PHE* 4.4 2.7 - - - -
181H ARG* 3.2 25.1 + - - +
182H TYR* 3.3 28.8 + - + +
184H GLU* 2.9 37.3 + - + -
195H LEU* 3.5 29.3 - - + +
224H LEU* 4.1 14.1 - - + -
227H ARG 3.5 27.1 - - - -
229H GLN* 3.8 24.0 - - - -
230H ILE* 4.1 15.9 - - + -
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Residues in contact with VAL 173 (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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133H LYS 3.4 4.0 - - - +
134H ILE* 3.7 3.0 - - - -
135H VAL 3.0 30.5 + - - +
137H LEU* 3.7 28.9 - - + +
140H ALA* 3.9 16.4 - - + -
143H PHE* 3.7 18.8 - - + -
171H LEU 4.0 2.2 + - - -
172H TRP* 1.3 73.3 - - - +
174H ASP* 1.3 74.7 + - - +
175H ARG* 4.1 7.8 - - + +
179H TYR 4.0 6.1 - - - +
180H PHE* 4.1 8.9 - - + -
12M ALA* 3.6 28.7 - - + -
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Residues in contact with ASP 174 (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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133H LYS* 3.0 31.0 - - - +
134H ILE* 3.5 19.2 - - + +
172H TRP 3.9 0.4 + - - -
173H VAL* 1.3 74.1 - - - +
175H ARG* 1.3 54.0 + - - +
176H SER* 3.1 8.7 + - - -
177H GLU* 4.2 12.2 - - - +
178H HIS* 2.7 36.4 + - - -
179H TYR* 2.8 26.2 + - + +
181H ARG* 2.7 37.8 + - - +
231M ARG* 4.8 2.3 + - - +
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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