Contacts of the strand formed by residues 260 - 267 (chain A) in PDB entry 1PVL
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 260 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187A THR* 3.5 37.2 - - + +
188A TYR* 3.3 21.7 - + + +
197A ARG 3.5 2.9 - - - +
198A GLN* 3.1 24.0 - - - +
255A PHE 3.8 0.3 - - - +
256A TRP* 3.5 14.1 - - - -
257A ASN* 2.7 60.9 + - - +
259A LEU* 1.3 81.2 - - + +
261A TRP* 1.3 77.1 + - - +
262A ILE* 3.6 8.7 - - + -
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Residues in contact with TRP 261 (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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72A ILE 3.8 1.6 - - - -
188A TYR* 3.5 13.2 - - - -
194A LEU* 4.1 13.1 - - + +
196A SER 3.4 19.3 - - - +
197A ARG* 3.0 30.9 + - - +
199A SER 2.8 28.4 + - - -
201A LEU 3.4 20.0 - - - -
202A ASN 4.4 0.4 - - - -
203A ALA* 3.3 45.1 - - + -
206A ASN* 3.3 20.7 - - + +
254A ASN* 4.0 9.4 - - + -
255A PHE 3.3 26.2 - - - -
256A TRP* 3.5 33.5 - + + -
260A HIS* 1.3 91.7 + - - +
262A ILE* 1.3 58.8 + - - +
402A MES 3.6 19.5 - - + -
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Residues in contact with ILE 262 (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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187A THR 3.8 11.7 - - - +
188A TYR 3.6 15.9 - - - +
189A GLY* 4.2 3.4 - - - +
194A LEU* 4.5 3.8 - - - -
254A ASN* 3.1 4.7 - - - +
255A PHE* 2.8 50.5 + - + +
257A ASN* 3.8 26.9 - - + +
260A HIS* 3.6 13.9 - - + -
261A TRP* 1.3 80.0 - - - +
263A GLY* 1.3 65.6 + - - +
264A ASN* 3.8 21.6 + - - +
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Residues in contact with GLY 263 (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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188A TYR 3.0 9.3 + - - -
189A GLY* 3.3 3.8 - - - -
190A ASN 2.8 35.2 + - - -
194A LEU* 4.2 8.6 - - - +
252A TYR* 3.8 6.5 - - - -
253A THR 3.2 10.8 - - - -
254A ASN* 4.2 1.3 - - - -
262A ILE* 1.3 75.0 - - - +
264A ASN* 1.3 70.7 + - - +
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Residues in contact with ASN 264 (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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189A GLY* 4.3 8.7 - - - -
190A ASN* 3.7 6.6 + - - +
251A ARG 3.9 0.3 - - - +
252A TYR* 3.3 10.0 - - - -
253A THR* 2.8 41.9 + - - +
255A PHE* 5.9 3.6 - - - +
262A ILE* 3.8 16.6 - - - +
263A GLY* 1.3 82.9 + - - +
265A ASN* 1.3 60.3 + - - +
266A TYR* 3.4 31.0 + - + +
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Residues in contact with ASN 265 (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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78A TRP* 3.0 30.0 + - - -
181A ARG* 2.9 30.7 + - - +
190A ASN* 3.6 25.6 + - - +
192A MET* 4.3 2.5 - - + -
250A ASP* 2.9 32.1 + - - +
251A ARG 3.5 7.8 - - - +
252A TYR* 3.8 9.0 - - + +
264A ASN* 1.3 77.7 - - - +
266A TYR* 1.3 64.8 + - - +
267A LYS* 3.9 5.0 + - - +
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Residues in contact with TYR 266 (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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250A ASP* 3.3 3.4 - - - -
251A ARG* 2.8 55.2 + - + +
253A THR* 3.6 31.2 + - + -
264A ASN* 3.4 32.7 + - + +
265A ASN* 1.3 74.5 - - - +
267A LYS* 1.3 63.7 + - - +
269A GLU* 3.6 19.1 - - + +
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Residues in contact with LYS 267 (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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167A GLU* 5.3 1.3 + - - -
181A ARG* 3.6 40.8 - - + +
182A ASP* 2.9 43.8 + - - +
250A ASP* 3.3 19.5 - - - +
265A ASN* 3.9 2.9 + - - +
266A TYR* 1.3 72.5 - - - +
268A ASP* 1.3 76.7 + - + +
269A GLU* 4.2 4.7 - - - +
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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