Contacts of the strand formed by residues 269 - 274 (chain A) in PDB entry 1EFA
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 SER 269 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A LEU* 4.4 1.8 - - - -
179A HIS* 3.3 28.9 + - - -
240A THR 2.8 10.8 + - - -
241A ALA* 3.2 7.6 - - - -
242A MET 2.9 20.0 + - - -
265A GLY 3.1 15.9 + - - +
268A ILE* 1.3 78.7 - - - +
270A VAL* 1.3 64.3 + - - +
328A THR 3.1 11.9 - - - -
329A THR* 3.6 24.6 - - - -
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Residues in contact with VAL 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A MET* 3.4 11.9 - - + +
244A VAL* 3.9 23.6 - - + -
250A ALA* 4.1 18.6 - - + +
253A ALA* 5.0 2.5 - - + -
254A MET* 4.4 11.0 - - + -
257A ILE* 3.6 28.9 - - + -
264A VAL* 4.3 8.5 - - + -
268A ILE 3.7 2.5 - - - +
269A SER* 1.3 81.4 - - - +
271A VAL* 1.3 71.1 + - - +
286A LEU* 4.1 5.4 - - + -
287A THR 4.1 0.3 - - - +
328A THR* 3.0 35.4 + - - -
329A THR* 3.1 10.7 - - - +
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Residues in contact with VAL 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A GLY* 4.6 13.0 - - - +
173A HIS* 4.7 4.5 - - + -
174A LEU* 3.9 23.1 - - + -
242A MET 2.9 11.7 + - - +
243A LEU* 4.0 16.6 - - + -
244A VAL* 2.8 31.9 + - - +
270A VAL* 1.3 84.6 - - - +
272A GLY* 1.3 72.9 + - - +
287A THR* 3.5 15.7 - - + +
288A THR* 4.4 4.9 - - - -
289A ILE* 4.7 8.5 - - + -
323A LEU* 5.0 1.6 - - + -
329A THR* 3.5 19.1 - - + -
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Residues in contact with GLY 272 (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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244A VAL 3.6 7.2 - - - -
246A ASN 4.4 0.9 - - - -
247A ASP* 3.7 9.6 - - - -
250A ALA* 4.2 15.9 - - - -
271A VAL* 1.3 81.4 - - - +
273A TYR* 1.3 64.7 + - - +
286A LEU* 3.8 2.5 - - - +
287A THR 2.9 13.6 + - - -
288A THR* 3.0 11.9 + - - -
289A ILE* 3.3 14.6 + - - +
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Residues in contact with TYR 273 (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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161A PHE* 5.8 0.5 - - - +
162A SER 4.2 1.9 + - - -
163A HIS* 3.8 17.8 - - - -
166A GLY* 3.2 29.6 - - - -
167A THR* 4.0 7.6 + - + -
197A ARG* 3.6 43.5 - - + -
201A TRP* 4.8 10.1 - + - -
244A VAL 3.7 5.2 - - - +
245A ALA 2.8 25.4 - - - +
246A ASN* 3.0 8.4 - - - -
247A ASP* 2.9 21.1 + - - -
272A GLY* 1.3 74.3 - - - -
274A ASP* 1.3 80.3 + - - +
288A THR* 3.4 1.1 - - - -
289A ILE* 3.8 31.9 - - + +
291A GLN* 3.6 27.9 + - + -
321A VAL* 5.0 2.6 - - - +
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Residues in contact with ASP 274 (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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74A HIS* 4.6 4.3 - - - -
197A ARG* 4.4 0.3 + - - -
246A ASN* 3.8 3.3 + - - +
247A ASP* 3.5 8.5 + - - +
248A GLN* 4.9 2.3 + - - +
273A TYR* 1.3 82.4 - - - +
275A ASP* 1.3 70.5 - - - +
276A THR* 3.7 20.4 - - + +
289A ILE 2.8 14.2 + - - -
290A LYS* 4.6 0.2 - - - +
291A GLN* 2.9 46.3 + - - +
293A PHE* 3.7 15.8 - - + -
901A NPF 2.4 42.9 + - - -
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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