Contacts of the strand formed by residues 269 - 274 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174B LEU* 4.3 2.0 - - - -
179B HIS* 3.3 24.8 + - - -
240B THR 2.9 15.7 + - - -
241B ALA* 3.1 6.4 - - - -
242B MET 2.8 23.9 + - - -
265B GLY 3.2 16.6 + - - +
268B ILE* 1.3 76.8 - - - +
270B VAL* 1.3 64.1 + - - +
328B THR 3.1 11.2 - - - -
329B THR* 3.5 24.6 - - - -
331B ALA 4.9 1.6 + - - -
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Residues in contact with VAL 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B MET* 3.5 11.2 - - + +
244B VAL* 3.9 24.2 - - + -
250B ALA* 4.1 17.7 - - + +
253B ALA* 5.0 2.5 - - + -
254B MET* 4.4 11.2 - - + -
257B ILE* 3.6 28.9 - - + -
264B VAL* 4.2 8.1 - - + -
268B ILE 3.8 3.1 - - - +
269B SER* 1.3 81.8 - - - +
271B VAL* 1.3 69.9 + - - +
286B LEU* 4.2 4.7 - - + -
287B THR 4.0 0.3 - - - +
328B THR* 2.9 40.0 + - - -
329B THR* 3.2 9.5 - - - +
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Residues in contact with VAL 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B GLY* 4.6 13.5 - - - +
173B HIS* 4.8 4.5 - - + -
174B LEU* 3.9 23.8 - - + -
242B MET 2.9 11.7 + - - +
243B LEU* 4.0 16.6 - - + -
244B VAL* 2.9 31.5 + - - +
270B VAL* 1.3 84.1 - - - +
272B GLY* 1.3 72.1 + - - +
287B THR* 3.5 15.5 - - + +
288B THR* 4.5 4.9 - - - -
289B ILE* 4.7 8.5 - - + -
323B LEU* 5.0 2.0 - - + -
329B THR* 3.6 18.2 - - + -
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Residues in contact with GLY 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244B VAL 3.6 7.4 - - - +
246B ASN 4.4 0.4 - - - -
247B ASP* 3.7 9.4 - - - -
250B ALA* 4.1 16.4 - - - -
271B VAL* 1.3 83.1 - - - +
273B TYR* 1.3 65.4 + - - +
286B LEU* 3.8 3.1 - - - +
287B THR 2.9 13.2 + - - -
288B THR* 3.1 10.4 + - - -
289B ILE* 3.3 14.0 + - - +
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Residues in contact with TYR 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161B PHE* 5.8 0.3 - - - +
162B SER 4.2 1.9 + - - -
163B HIS* 3.8 18.7 + - - -
166B GLY* 3.3 29.3 + - - -
167B THR* 4.1 7.3 + - + -
197B ARG* 3.6 40.1 - - + +
201B TRP* 4.8 9.2 - + - -
244B VAL 3.7 5.2 - - - +
245B ALA 2.9 25.8 - - - +
246B ASN* 3.0 4.1 - - - -
247B ASP* 2.8 29.6 + - - +
272B GLY* 1.3 73.7 - - - -
274B ASP* 1.3 78.4 + - - +
288B THR* 3.4 2.0 - - - -
289B ILE* 3.8 32.5 - - + +
291B GLN* 3.6 33.1 + - + -
321B VAL* 5.0 2.8 - - - +
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Residues in contact with ASP 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B HIS* 4.6 4.3 - - - -
197B ARG* 4.5 0.3 + - - -
246B ASN* 3.7 3.6 + - - +
247B ASP* 3.6 8.6 + - - +
248B GLN* 4.8 2.4 - - - +
273B TYR* 1.3 83.8 - - - +
275B ASP* 1.3 69.7 + - - +
276B THR* 3.7 19.3 - - + +
289B ILE 2.7 13.8 + - - -
290B LYS* 4.6 0.3 - - - +
291B GLN* 2.9 47.2 + - - +
293B PHE* 3.8 17.1 - - + -
902B NPF 2.6 41.9 + - - -
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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
------------------------------------------------------------
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