Contacts of the strand formed by residues 293 - 296 (chain B) in PDB entry 1LT8
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 293 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225B LEU* 4.4 4.9 - - + -
228B VAL* 4.1 15.3 - - + -
244B LEU* 3.6 22.2 - - + +
246B SER* 3.5 26.5 - - - +
288B ALA* 2.9 26.5 + - + +
289B TYR* 3.8 2.6 - - - -
291B LEU* 4.0 23.3 - - + -
292B GLY* 1.3 78.9 - - - +
294B ARG* 1.3 77.0 + - - +
295B TYR 3.6 12.8 - - - +
296B ILE* 3.7 19.3 - - + +
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Residues in contact with ARG 294 (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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17B LEU* 3.8 16.2 - - + +
20B GLY* 4.4 13.7 + - - +
21B GLU 3.7 13.9 - - - +
22B ILE* 3.5 23.7 - - - +
23B VAL* 2.6 35.2 + - - +
243B HIS* 5.7 6.5 - - + -
244B LEU 3.4 6.1 + - - +
289B TYR* 3.0 53.8 + - - +
292B GLY* 3.2 25.3 + - - +
293B VAL* 1.3 90.2 + - - +
295B TYR* 1.3 57.3 + - - +
296B ILE* 3.5 5.6 - - - -
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Residues in contact with TYR 295 (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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13B ILE* 4.2 18.4 - - + -
17B LEU* 4.6 6.5 - - + +
23B VAL* 3.3 11.7 - - + -
25B GLY* 4.1 12.9 - - - -
26B ASP 5.6 0.2 + - - -
70B VAL* 3.6 32.2 - - + +
72B GLN* 4.4 4.9 + - - -
155B PHE* 3.8 23.8 - + - -
157B ILE* 3.9 9.0 - - - +
212B ILE* 4.5 15.0 - - + -
244B LEU 3.3 13.2 + - - +
245B MET* 3.3 49.2 - - + +
246B SER 3.0 22.0 + - - +
247B GLN* 3.9 13.8 + - - -
293B VAL* 3.6 1.6 - - - +
294B ARG* 1.3 77.3 - - - +
296B ILE* 1.3 59.8 + - - +
297B GLY 4.5 3.4 - - - -
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Residues in contact with ILE 296 (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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22B ILE* 4.0 11.2 - - + -
23B VAL 2.8 9.3 + - - +
24B ILE* 3.3 12.4 - - - +
25B GLY 2.8 19.2 + - - -
246B SER* 3.9 2.2 - - - +
284B TYR* 3.4 30.1 - - + +
285B ALA* 4.1 12.8 - - - +
288B ALA* 4.1 9.2 - - + -
289B TYR* 4.1 4.0 - - + +
293B VAL* 3.7 32.8 - - + +
294B ARG 4.2 1.3 - - - -
295B TYR* 1.3 75.9 - - - +
297B GLY* 1.3 58.1 + - - +
310B ILE* 3.7 23.0 - - + +
314B LEU* 3.6 29.6 - - + -
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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