Contacts of the strand formed by residues 170 - 176 (chain X) in PDB entry 1P7G
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 GLN 170 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168U ASP* 3.4 23.2 + - - +
170U GLN* 3.4 17.2 - - - +
218U ILE* 3.8 23.7 - - + +
145X VAL* 3.1 6.6 - - - -
146X TYR* 2.8 38.1 + - + +
148X PRO* 5.5 0.2 - - + -
168X ASP 3.0 22.4 + - - -
169X ALA* 1.3 82.2 + - - +
171X VAL* 1.3 63.3 - - - +
172X LEU* 3.5 2.8 + - + +
213X ALA* 4.1 19.3 - - + -
217X GLN 3.9 7.4 - - - +
218X ILE* 3.2 13.5 - - - +
219X ALA* 2.9 32.4 + - + +
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Residues in contact with VAL 171 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167U ALA* 4.1 23.1 - - + -
168U ASP* 3.0 16.9 + - - +
89X LEU* 4.4 7.2 - - + -
92X ILE* 3.8 31.5 - - + +
143X ILE* 4.3 22.0 - - + -
144X LEU 3.8 4.5 - - - +
145X VAL* 4.2 3.1 - - + -
165X HIS* 4.9 1.3 - - + +
169X ALA 5.0 1.6 - - - +
170X GLN* 1.3 71.9 - - - +
172X LEU* 1.3 64.0 + - - +
173X LEU 4.3 6.7 - - - +
174X ALA* 4.2 23.8 - - + -
209X ARG* 3.8 14.7 - - - -
219X ALA* 4.0 8.5 - - - +
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Residues in contact with LEU 172 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92X ILE* 5.0 0.4 - - - -
96X ASN* 3.2 20.0 + - - -
111X ILE* 4.5 4.3 - - + -
144X LEU* 2.8 23.9 + - + +
145X VAL 4.3 0.9 - - - -
146X TYR* 4.0 13.5 - - + +
153X LEU* 3.6 30.7 - - + -
170X GLN* 3.6 24.0 - - + +
171X VAL* 1.3 79.5 - - - +
173X LEU* 1.3 59.1 + - - +
206X VAL* 3.9 23.4 - - + +
209X ARG* 3.7 38.6 - - + +
210X LEU* 3.7 24.7 - - + +
213X ALA* 4.4 0.2 - - + -
219X ALA* 4.4 0.7 - - + -
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Residues in contact with LEU 173 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96X ASN* 3.1 25.8 - - + +
125X PHE* 4.4 10.8 - - + -
129X PHE* 4.2 10.0 - - + -
143X ILE* 3.0 5.7 - - - +
144X LEU* 2.7 45.2 + - + +
171X VAL* 4.5 1.8 - - - -
172X LEU* 1.3 78.2 - - - +
174X ALA* 1.3 61.2 + - - +
197X TRP* 3.6 41.1 - - + -
198X TRP* 4.5 1.3 - - + -
201X VAL* 3.9 9.9 - - + -
203X TRP* 3.6 34.3 - - + -
206X VAL* 3.9 15.9 - - + -
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Residues in contact with ALA 174 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89X LEU* 4.6 11.0 - - + +
92X ILE* 4.8 3.1 - - + -
93X PHE* 2.9 28.4 - - + +
96X ASN* 2.7 16.9 + - - +
141X TRP* 3.9 16.2 - - + -
142X ALA 3.5 3.8 - - - -
143X ILE* 3.6 17.5 - - + -
171X VAL* 4.2 11.9 - - + -
173X LEU* 1.3 76.8 - - - +
175X LEU* 1.3 60.3 + - - +
197X TRP* 4.2 7.1 - - - -
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Residues in contact with LEU 175 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93X PHE* 4.0 1.6 - - + -
129X PHE* 3.8 19.4 - - + -
133X ALA* 3.5 29.4 - - + -
141X TRP* 3.2 9.0 - - - -
142X ALA* 2.7 33.4 + - + +
174X ALA* 1.3 71.7 - - - +
176X ASP* 1.3 67.4 + - - +
177X VAL* 3.5 2.8 + - + +
193X TYR* 3.6 25.8 - - + +
194X VAL* 3.7 26.9 - - + -
197X TRP* 3.6 44.0 - - + +
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Residues in contact with ASP 176 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42X HIS* 2.8 33.4 + - + -
90X HIS* 3.3 13.5 + - - -
93X PHE* 3.4 21.5 - - + -
141X TRP* 3.5 28.4 - - + -
175X LEU* 1.3 73.4 - - - +
177X VAL* 1.3 60.2 + - - +
178X TRP* 2.8 31.7 + - - +
180X HIS* 4.1 2.9 + - - -
181X ALA* 3.8 6.0 - - + +
193X TYR* 2.8 30.7 + - - -
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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