Contacts of the strand formed by residues 171 - 179 (chain A) in PDB entry 3JRQ
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 HIS 171 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125A SER* 3.3 41.9 + - - -
127A PRO* 3.4 28.1 - - + +
148A ILE 3.7 4.3 - - - +
149A PRO* 3.6 10.1 - - + -
150A ARG* 3.2 31.1 + - - -
151A PHE* 4.5 1.6 - - - -
169A ALA 3.1 20.4 + - - -
170A ALA* 1.3 72.1 - - - +
172A PHE* 1.3 60.4 + - - +
173A PHE* 3.6 24.0 - - + -
247A ALA 3.7 1.7 - - - +
248A VAL* 3.3 6.1 - - - +
249A VAL* 2.9 46.0 + - + +
250A PHE 6.1 0.6 - - - -
251A PRO* 6.5 0.4 - - + -
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Residues in contact with PHE 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A SER* 4.1 7.9 - - - -
147A THR* 3.5 0.5 - - - -
148A ILE* 2.8 46.4 + - + +
151A PHE* 3.7 27.1 - + + -
170A ALA 4.2 0.4 + - - -
171A HIS* 1.3 71.6 - - - +
173A PHE* 1.3 70.9 + - - +
174A GLY 3.9 11.7 - - - -
176A TYR* 3.2 28.3 - - - -
192A MET* 3.8 4.7 - - + -
193A HIS* 3.6 40.8 - - + -
196A LEU* 3.7 25.4 - - + -
246A VAL* 3.5 32.1 - - + -
247A ALA 3.7 2.0 - - - -
248A VAL* 4.5 3.4 - - + +
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Residues in contact with PHE 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A PRO* 4.2 16.4 - - + -
129A TYR* 3.6 35.7 - + + -
146A SER 3.3 5.2 - - - +
147A THR* 3.7 20.9 - - + -
148A ILE 5.1 1.6 - - - -
149A PRO 6.0 0.2 - - - -
171A HIS* 3.6 31.9 - - + -
172A PHE* 1.3 85.6 - - - +
174A GLY* 1.3 58.3 + - - +
246A VAL* 3.2 5.0 - - - +
247A ALA* 2.7 51.4 + - + +
249A VAL* 3.9 22.0 - - + -
344A LEU* 3.7 12.1 - - + +
418A VAL* 3.9 20.9 - - + -
420A VAL* 4.4 17.3 - - + -
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Residues in contact with GLY 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A VAL* 3.3 5.4 - - - +
146A SER 2.8 36.0 + - - +
172A PHE* 3.9 3.3 - - - -
173A PHE* 1.3 73.8 - - - +
175A VAL* 1.3 66.8 + - - +
176A TYR* 3.7 25.8 - - - -
245A VAL 3.3 8.3 - - - -
246A VAL* 4.3 1.3 - - - -
418A VAL* 4.6 0.4 - - - +
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Residues in contact with VAL 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A ALA 3.7 3.4 - - - +
145A VAL* 4.7 4.9 - - + -
174A GLY* 1.3 79.1 - - - +
176A TYR* 1.4 63.4 + - - +
177A ASP* 4.1 0.4 - - + -
243A THR* 4.1 2.6 + - - -
244A SER* 3.5 3.3 - - - -
245A VAL* 2.9 41.2 + - + +
262A SER* 4.5 5.3 + - - +
344A LEU* 3.6 32.3 - - + +
345A ALA* 4.3 1.1 - - - -
346A SER* 3.9 28.7 - - - +
416A SER* 4.1 19.5 - - - +
417A VAL 5.0 0.2 - - - -
418A VAL* 3.9 17.9 - - + +
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Residues in contact with TYR 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A ASP* 3.2 3.6 - - - -
144A ALA 2.8 47.1 + - - +
146A SER* 3.7 19.7 + - - -
172A PHE* 3.2 35.3 - - - -
174A GLY* 3.7 15.3 - - - -
175A VAL* 1.4 78.2 - - - +
177A ASP* 1.3 60.2 + - - +
185A ALA* 3.5 19.0 - - + +
188A CYS* 3.4 24.8 + - + -
189A ARG* 3.8 19.5 - - - -
192A MET* 3.4 10.0 - - + +
193A HIS* 4.8 0.3 + - - -
242A SER* 3.6 13.2 - - - +
243A THR 3.4 4.3 - - - -
244A SER* 3.5 29.4 - - - -
246A VAL* 4.1 9.9 - - + -
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Residues in contact with ASP 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A ASP* 2.6 27.9 - - - +
175A VAL* 5.3 0.2 - - + -
176A TYR* 1.3 71.8 - - - +
178A GLY* 1.3 69.6 + - - +
179A HIS* 3.9 3.1 + - - -
242A SER* 3.4 4.3 + - - -
243A THR* 3.0 46.9 + - - +
261A ASP* 4.2 1.6 - - - +
262A SER* 3.7 9.1 + - - +
311A MET* 5.7 1.1 - - - +
346A SER* 3.9 17.6 - - - -
347A ASP* 3.4 25.8 + - - +
413A ASP* 3.6 12.6 - - - +
414A ASN* 5.0 2.1 - - - +
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Residues in contact with GLY 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A GLU* 2.6 37.4 + - - +
176A TYR 3.6 1.8 + - - -
177A ASP* 1.3 84.7 + - - +
179A HIS* 1.3 62.1 + - - +
181A GLY 3.9 8.5 - - - -
185A ALA* 3.6 11.2 - - - +
241A GLY 3.3 11.7 - - - -
242A SER* 3.6 1.9 + - - -
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Residues in contact with HIS 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A GLU* 3.6 5.4 - - - -
177A ASP 3.9 3.4 + - - -
178A GLY* 1.3 78.2 - - - +
180A GLY* 1.3 60.5 + - - +
181A GLY 3.0 9.3 + - - +
239A THR 5.0 0.9 - - - -
240A VAL* 3.5 0.5 - - - -
241A GLY* 2.7 35.8 + - - +
242A SER* 3.4 25.6 - - - -
309A LEU* 4.2 16.8 - - + +
311A MET* 3.5 37.1 - - + +
314A SER* 4.1 1.3 - - - -
317A ASP* 2.4 39.8 + - - -
112B SER* 3.7 10.3 - - - +
113B GLY* 4.3 11.4 - - - -
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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