Contacts of the strand formed by residues 175 - 183 (chain H) in PDB entry 1JH0
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 MET 175 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169H VAL* 3.6 4.2 - - - -
170H ASP* 2.9 35.7 + - + +
173H GLU* 3.7 15.9 - - + +
174H GLN* 1.3 75.8 - - - +
176H ALA* 1.3 71.8 - - - +
177H ARG* 3.1 55.5 + - + +
194H GLN* 4.3 7.4 - - - +
227L LEU* 4.1 28.5 - - + -
8M SER* 5.5 6.5 - - - +
12M VAL* 4.8 7.5 - - - +
232M GLU* 3.7 10.5 - - - +
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Residues in contact with ALA 176 (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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167H ILE* 4.3 16.6 - - + -
168H TRP 4.2 5.2 - - - -
169H VAL* 4.8 2.0 - - - +
175H MET* 1.3 84.5 - - - +
177H ARG* 1.3 62.4 + - - +
193H MET* 3.5 37.0 - - + +
194H GLN* 5.0 0.7 + - - -
10M VAL* 4.2 22.8 + - + +
12M VAL* 4.8 8.9 - - + +
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Residues in contact with ARG 177 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131H ILE* 3.3 27.1 - - + +
168H TRP 3.2 10.5 + - - +
170H ASP* 2.8 26.6 + - - +
173H GLU* 3.9 14.5 + - - -
175H MET* 3.1 41.0 + - + +
176H ALA* 1.3 77.1 - - - +
178H PHE* 1.3 83.0 + - + +
192H PRO* 3.7 1.4 - - - +
193H MET* 3.0 25.4 + - - +
194H GLN* 4.0 13.0 + - - +
226L THR* 5.0 0.2 + - - -
230M GLY* 5.1 3.6 - - - -
232M GLU* 3.3 25.5 + - - +
233M ARG* 3.8 41.9 - - - +
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Residues in contact with PHE 178 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131H ILE* 4.4 15.5 - - + -
167H ILE* 3.6 6.2 - - - +
168H TRP* 2.9 40.7 + - + +
177H ARG* 1.3 93.8 - - + +
179H LEU* 1.3 66.9 + - - +
190H LEU* 3.8 33.2 - - + -
191H LEU 3.4 19.7 - - - -
192H PRO* 3.6 25.4 - - + -
193H MET* 4.2 4.7 - - - +
225H VAL* 4.7 8.3 - - + -
230H GLU* 4.1 36.6 - - + -
233H ILE* 4.6 7.4 - - + -
234H CYS* 4.4 13.2 - - - -
233M ARG* 5.4 1.8 - - - -
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Residues in contact with LEU 179 (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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148H PRO* 3.8 36.1 - - + -
153H VAL* 5.7 1.3 - - + -
164H VAL* 4.0 17.5 - - + -
166H ASP 3.8 0.9 - - - -
167H ILE* 3.9 13.5 - - + -
178H PHE* 1.3 80.5 - - - +
180H GLU* 1.3 63.2 + - - +
181H VAL* 3.3 12.9 + - + +
190H LEU* 4.5 2.0 - - - -
191H LEU* 3.1 34.1 + - + +
193H MET* 3.9 32.1 - - + -
196H VAL* 4.2 9.6 - - + -
198H VAL* 5.0 0.7 - - + -
203H VAL* 4.2 26.2 - - + -
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Residues in contact with GLU 180 (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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135H LYS* 3.9 20.4 + - - -
164H VAL* 3.5 4.5 - - - -
165H VAL* 3.0 39.4 + - + +
166H ASP* 2.9 18.1 + - - +
168H TRP* 2.6 47.3 + - + +
178H PHE 4.1 1.4 - - - -
179H LEU* 1.3 70.2 - - - +
181H VAL* 1.3 60.4 + - - +
188H THR* 3.4 37.1 + - + +
189H ARG 3.5 4.3 - - - +
190H LEU* 3.8 10.5 - - + -
222H PRO 4.9 2.6 - - - +
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Residues in contact with VAL 181 (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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153H VAL* 4.1 18.8 - - + -
161H ALA 5.3 0.4 - - - -
162H GLY* 4.0 7.6 - - - -
163H LYS 2.9 31.0 - - - +
164H VAL* 4.7 1.6 - - + -
179H LEU* 3.5 20.0 - - + +
180H GLU* 1.3 74.6 - - - +
182H GLU* 1.3 66.0 + - - +
183H LEU* 4.5 11.1 - - + +
187H SER 3.7 0.3 - - - +
188H THR* 2.9 27.0 - - - -
189H ARG* 2.8 21.4 + - + +
191H LEU* 3.9 27.1 - - + -
213H PHE* 5.5 3.4 - - + -
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Residues in contact with GLU 182 (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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162H GLY* 3.0 25.3 - - - -
163H LYS* 2.8 24.9 + - + +
165H VAL* 3.6 27.7 - - + +
181H VAL* 1.3 74.0 - - - +
183H LEU* 1.3 73.9 + - - +
186H GLY* 4.1 23.3 - - - +
187H SER 3.6 3.4 - - - +
188H THR* 3.6 8.8 - - + +
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Residues in contact with LEU 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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161H ALA 3.5 19.3 - - - +
162H GLY* 5.0 1.3 - - - -
181H VAL* 4.5 10.8 - - + +
182H GLU* 1.3 85.8 - - - +
184H LYS* 1.3 56.1 + - - +
185H ASP* 3.0 13.0 - - - +
186H GLY* 2.8 24.3 + - - -
187H SER* 2.8 18.2 + - - +
189H ARG* 3.1 51.1 - - + +
213H PHE* 3.9 25.4 - - + -
214H ALA* 4.1 17.3 - - + +
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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