Contacts of the strand formed by residues 255 - 260 (chain A) in PDB entry 4LG8
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 GLN 255 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249A PHE* 3.3 5.0 - - - -
250A ASP* 2.8 30.7 + - - +
253A SER* 3.2 34.0 + - - +
254A GLU* 1.3 82.9 + - - +
256A ILE* 1.3 67.8 + - - +
257A LEU* 3.5 10.0 + - + +
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Residues in contact with ILE 256 (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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215A GLY 3.8 23.1 - - - +
216A LEU* 4.1 13.9 - - + +
247A VAL* 4.0 10.3 - - + -
248A VAL 3.6 6.5 - - - +
249A PHE* 4.1 15.0 - - + -
254A GLU 4.4 0.2 + - - -
255A GLN* 1.3 79.1 + - - +
257A LEU* 1.3 64.4 + - - +
258A ALA* 3.5 24.7 - - - +
259A THR* 3.7 17.0 - - - +
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Residues in contact with LEU 257 (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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236A LYS* 4.1 30.3 - - + +
248A VAL* 2.8 34.4 + - + +
250A ASP* 4.2 17.9 - - + +
253A SER* 5.0 1.3 - - - +
255A GLN* 4.1 19.5 - - + +
256A ILE* 1.3 76.2 - - - +
258A ALA* 1.3 62.5 + - + +
293A VAL* 4.9 10.9 - - + +
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Residues in contact with ALA 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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246A VAL 4.0 0.3 - - - +
247A VAL* 3.4 4.9 - - - -
248A VAL* 3.1 30.5 + - + -
256A ILE* 3.4 9.1 - - - +
257A LEU* 1.3 83.0 - - - +
259A THR* 1.3 62.6 + - - +
260A LEU* 4.0 24.2 - - + -
293A VAL* 4.3 25.8 - - + +
296A ALA* 4.6 7.9 - - + -
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Residues in contact with THR 259 (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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216A LEU 5.0 1.7 + - - +
245A ASN* 3.8 33.0 - - + +
246A VAL 3.7 2.5 - - - -
247A VAL* 4.2 12.2 - - + +
256A ILE* 3.7 18.7 - - - +
258A ALA* 1.3 73.4 + - - +
260A LEU* 1.3 62.1 + - - +
261A LYS* 3.7 13.3 + - - +
296A ALA* 5.3 3.7 - - - +
611A UNX 3.1 14.7 - - - -
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Residues in contact with LEU 260 (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 LYS 4.5 0.5 - - - +
245A ASN* 3.5 4.3 - - - -
246A VAL* 2.7 53.8 + - + +
248A VAL* 4.5 11.4 - - + -
258A ALA* 4.1 15.5 - - + -
259A THR* 1.3 73.4 - - - +
261A LYS* 1.3 60.6 + - - +
262A GLY 4.2 0.2 + - - -
279A VAL* 3.7 31.0 - - + -
291A TRP* 3.5 35.5 - - + -
292A SER 4.2 5.2 - - - +
293A VAL* 5.1 2.5 - - + -
296A ALA* 3.6 39.3 - - + +
297A SER 4.0 3.6 - - - +
611A UNX 3.7 1.8 - - - -
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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