Contacts of the strand formed by residues 254 - 258 (chain A) in PDB entry 1EKV
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 LEU 254 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246A TYR* 3.7 37.2 - - + +
247A TRP* 2.9 30.5 - - - +
248A THR* 4.0 12.9 - - + +
252A GLY 3.9 3.0 + - - -
253A VAL* 1.3 79.4 - - - +
255A GLU* 1.3 63.9 + - - +
284A PHE* 3.9 11.9 - - + +
285A ARG 3.4 17.3 + - - -
306A ARG* 4.4 19.5 - - - +
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Residues in contact with GLU 255 (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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246A TYR* 3.5 7.5 - - - -
247A TRP* 2.9 63.7 + - + +
249A HIS* 4.0 5.8 - - + -
253A VAL 3.6 11.2 - - - +
254A LEU* 1.3 77.6 - - - +
256A LEU* 1.3 60.1 + - - +
257A VAL* 3.3 10.9 - - - +
284A PHE* 4.5 2.2 - - - -
285A ARG* 2.5 56.8 + - + +
287A VAL* 3.4 6.2 - - - +
289A ARG* 2.9 28.6 + - - -
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Residues in contact with LEU 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A PHE* 4.0 30.3 - - + -
245A VAL 3.3 20.4 - - - +
246A TYR* 4.2 2.9 - - + -
255A GLU* 1.3 73.0 - - - +
257A VAL* 1.3 59.2 + - - +
274A LEU 4.8 1.8 - - - +
275A LEU* 5.5 1.8 - - + +
278A ALA* 3.9 18.4 - - + -
284A PHE* 3.5 20.1 - - + -
285A ARG 2.7 9.1 + - - +
286A VAL* 3.5 9.5 - - + +
287A VAL* 2.9 26.9 + - - +
309A PHE* 4.2 7.0 - - + -
341A LEU* 3.8 19.3 - - + -
345A PHE* 3.7 29.8 - - + -
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Residues in contact with VAL 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A PHE* 3.4 4.4 - - - +
245A VAL* 2.7 55.7 + - + +
247A TRP* 3.5 22.0 - - + +
255A GLU* 3.3 13.2 - - - +
256A LEU* 1.3 73.3 - - - +
258A THR* 1.3 67.4 - - - +
275A LEU* 6.3 0.4 - - - -
287A VAL* 3.3 14.6 - - + +
289A ARG* 3.8 40.4 - - + +
291A ILE* 3.5 24.0 - - + +
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Residues in contact with THR 258 (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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242A ASN* 4.8 1.0 - - - +
243A ILE 2.6 22.0 + - - -
244A PHE* 3.6 33.9 - - + -
257A VAL* 1.3 80.5 - - - +
259A PRO* 1.3 76.5 + - - +
265A ILE* 5.9 0.2 - - - +
271A ARG* 3.9 28.4 + - - +
275A LEU* 4.2 15.9 - - + -
287A VAL 3.3 2.4 + - - +
288A GLU* 3.3 9.5 - - + -
289A ARG 3.3 16.8 + - - -
291A ILE* 4.4 0.2 - - - -
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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