Contacts of the strand formed by residues 276 - 279 (chain A) in PDB entry 3SE3
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 TYR 276 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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234A TRP* 3.6 9.9 - + - -
235A LEU 3.2 6.5 - - - +
236A HIS* 3.1 42.3 - + - -
237A ALA* 3.7 6.7 - - - +
271A PHE* 3.2 53.3 - + + -
272A GLN* 2.8 35.9 + - - +
273A LYS 4.1 4.5 + - - -
274A GLY* 3.4 26.4 - - - -
275A ILE* 1.3 75.6 - - - +
277A LEU* 1.3 61.3 + - - +
278A LEU* 5.0 7.4 - - + +
296A LYS* 3.1 29.1 - - - +
297A PHE 3.5 9.1 + - - +
299A THR* 4.5 4.3 - - - -
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Residues in contact with LEU 277 (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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234A TRP* 3.0 6.1 - - - -
235A LEU* 2.4 66.3 + - + +
237A ALA* 4.2 14.1 - - + +
240A LYS* 3.8 31.6 - - + -
250A TRP* 3.5 3.7 - - + -
276A TYR* 1.3 67.3 - - - +
278A LEU* 1.3 65.2 + - - +
294A GLU* 2.8 33.7 - - + +
295A ILE 3.1 15.5 - - - +
296A LYS* 3.7 17.9 - - + -
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Residues in contact with LEU 278 (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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210A VAL* 4.4 22.7 - - + -
232A VAL* 5.7 0.9 - - + -
233A GLN 3.7 4.9 - - - +
234A TRP* 3.3 23.8 - - + -
250A TRP* 4.2 1.8 - - - -
253A ILE* 4.6 11.2 - - + -
271A PHE* 4.7 10.5 - - + -
276A TYR* 5.0 7.0 - - + +
277A LEU* 1.3 87.5 - - - +
279A ARG* 1.3 61.5 + - - +
280A VAL* 5.8 1.3 - - + -
293A GLU 3.9 1.0 - - - +
294A GLU* 3.1 29.5 - - - +
295A ILE* 2.9 29.2 + - + +
297A PHE* 5.6 8.5 - - + -
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Residues in contact with ARG 279 (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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232A VAL* 3.6 3.5 - - - +
233A GLN* 2.5 60.8 + - + +
250A TRP* 3.0 65.3 - - + +
278A LEU* 1.3 75.5 - - - +
280A VAL* 1.3 65.7 + - - +
291A TRP* 3.3 44.9 - - + +
292A SER* 3.6 14.8 - - - +
294A GLU* 4.1 16.2 + - + -
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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