Contacts of the strand formed by residues 291 - 296 (chain F) in PDB entry 3EI4
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 VAL 291 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246F THR* 2.6 35.0 + - - +
261F ALA* 3.5 28.0 - - + -
262F SER 3.2 17.1 + - - +
263F VAL* 4.9 0.2 - - - -
265F GLN 4.4 1.8 - - - -
266F THR 4.1 5.6 - - - +
267F VAL* 3.8 10.5 - - + -
287F HIS* 3.4 44.9 - - + +
289F HIS 4.1 1.1 - - - +
290F PRO* 1.3 77.6 - - - +
292F ASN* 1.3 58.1 + - - +
293F ALA 3.7 17.5 - - - +
305F THR* 4.6 2.9 - - + -
306F THR 3.8 7.2 - - - +
307F ASP* 4.8 2.5 - - + -
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Residues in contact with ASN 292 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246F THR* 3.6 21.8 - - - +
247F HIS* 4.0 0.3 - - - +
290F PRO* 3.8 0.9 + - - +
291F VAL* 1.3 75.8 - - - +
293F ALA* 1.3 64.9 + - + +
306F THR 2.8 12.9 + - - +
307F ASP 3.3 15.9 + - - +
308F GLN* 3.4 37.0 + - - +
331F HIS* 4.7 3.2 + - - -
332F ARG 4.9 4.0 + - - -
339F PRO* 3.9 26.2 - - + +
340F ILE 3.4 28.8 + - - +
341F LYS* 3.5 16.6 + - + -
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Residues in contact with ALA 293 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247F HIS* 3.3 27.4 - - + +
291F VAL* 3.5 7.6 - - - +
292F ASN* 1.3 84.1 - - - +
294F ALA* 1.3 60.9 + - - +
295F CYS* 5.3 2.0 - - - +
304F LEU 3.5 2.2 - - - +
305F THR* 3.5 1.4 - - - -
306F THR* 2.7 39.9 + - - +
341F LYS* 3.7 26.2 - - + -
342F ALA 5.2 3.6 - - - +
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Residues in contact with ALA 294 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247F HIS* 3.6 20.9 + - - +
249F ALA* 3.8 7.4 - - - +
259F ALA* 4.6 6.3 - - + +
261F ALA* 3.7 20.4 - - + +
267F VAL* 3.8 17.5 - - + -
293F ALA* 1.3 76.4 - - - +
295F CYS* 1.3 60.3 + - - +
303F LEU* 3.9 13.6 - - + +
304F LEU 3.2 6.3 - - - -
305F THR* 3.8 18.2 - - - +
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Residues in contact with CYS 295 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247F HIS* 3.8 22.9 - - + +
249F ALA* 4.4 5.6 - - + -
293F ALA* 5.7 2.0 - - - -
294F ALA* 1.3 76.5 - - - +
296F PHE* 1.3 60.2 + - - +
303F LEU* 3.6 5.8 - - - +
304F LEU* 2.8 38.0 + - - +
342F ALA 3.9 21.8 - - - -
343F ALA* 4.5 8.3 - - - -
344F TRP* 3.0 24.4 + - - -
399F GLU* 5.7 2.0 - - - -
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Residues in contact with PHE 296 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249F ALA* 3.4 24.7 - - + +
250F LEU 3.9 3.1 - - - -
251F ASN* 3.2 51.4 - - - +
252F PRO* 3.7 17.9 - - + +
257F PHE* 3.6 22.4 - + - -
258F LEU 4.7 0.2 - - - -
259F ALA* 3.6 19.3 - - + -
269F ILE* 5.5 1.6 - - + -
295F CYS* 1.3 76.7 - - - +
297F SER* 1.3 65.1 + - - +
298F PRO* 3.8 1.4 - - - +
300F GLY* 3.8 4.5 - - - -
302F ARG 3.6 12.8 - - - -
303F LEU* 3.5 16.4 - - + -
320F TRP* 3.7 23.1 - + - -
344F TRP* 3.0 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