Contacts of the strand formed by residues 276 - 280 (chain A) in PDB entry 1LCG
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 CYS 276 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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259A ALA* 3.5 6.1 - - - +
260A LEU* 2.7 54.5 + - - +
272A CYS* 2.0 51.6 - - + -
275A GLY* 1.4 71.8 - - - +
277A GLN* 1.4 62.6 + - - +
366A PRO* 3.8 23.8 - - + +
368A TRP* 4.0 9.2 - - + -
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Residues in contact with GLN 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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251A THR* 2.7 33.0 + - - +
252A LYS* 5.3 1.2 - - - +
257A GLN* 2.9 21.0 + - - +
258A ILE 3.5 10.9 + - - +
259A ALA* 4.1 11.3 - - - +
260A LEU* 4.8 0.2 - - - -
276A CYS* 1.4 89.8 - - - +
278A ALA* 1.4 60.8 + - - +
365A GLY* 6.4 0.4 - - - -
366A PRO 3.3 9.7 + - - +
367A LEU* 3.3 23.4 - - + -
368A TRP* 3.0 21.7 + - - +
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Residues in contact with ALA 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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256A TRP 4.0 0.2 - - - +
257A GLN* 3.3 3.8 - - - +
258A ILE* 2.9 46.5 + - + +
260A LEU* 3.6 31.2 - - + -
277A GLN* 1.4 75.7 - - - +
279A ILE* 1.4 64.7 + - - +
367A LEU* 4.2 0.4 - - - -
368A TRP 3.1 11.9 - - - +
370A LEU* 4.5 14.1 - - + -
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Residues in contact with ILE 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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57A THR* 3.7 26.5 - - - +
97A THR 5.8 0.2 - - - +
98A GLY* 5.7 1.8 - - - -
255A TYR* 3.9 28.7 - - + -
256A TRP 3.5 9.2 - - - +
257A GLN* 3.3 30.1 - - + +
278A ALA* 1.4 74.0 - - - +
280A VAL* 1.4 77.2 + - - +
281A ASP* 3.5 9.9 + - + +
367A LEU* 4.2 22.9 - - + -
368A TRP 3.0 7.5 + - - -
369A ILE* 3.5 13.5 - - + +
370A LEU* 2.9 25.4 + - - -
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Residues in contact with VAL 280 (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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97A THR* 3.0 21.7 + - + +
256A TRP* 3.0 21.7 + - + +
258A ILE* 4.9 18.4 - - + -
279A ILE* 1.4 79.2 - - - +
281A ASP* 1.4 61.1 + - - +
282A THR* 5.2 0.4 - - - +
370A LEU* 3.7 17.3 - - + +
375A ILE* 3.8 24.7 - - + -
380A SER* 5.1 2.7 - - - +
382A PHE* 3.6 35.4 - - + -
389A VAL* 5.0 15.9 - - + -
391A LEU* 6.1 4.3 - - + -
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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