Contacts of the strand formed by residues 286 - 291 (chain G) in PDB entry 1GLE
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 286 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129G GLY 4.6 2.3 - - - +
131G VAL* 5.2 6.8 - - - +
282G SER* 3.1 31.1 + - - +
284G ASN 4.0 0.9 - - - +
285G GLY* 1.3 90.6 - - - +
287G LEU* 1.3 67.6 + - - +
288G THR* 4.1 0.9 + - - -
302G LEU* 5.1 4.9 - - + -
303G GLU 3.1 21.5 - - - +
304G GLY* 3.3 18.6 - - - -
353G ALA* 3.9 2.2 - - + -
354G PRO* 5.7 0.2 - - + -
391G VAL* 3.7 14.8 - - + +
394G ALA* 3.5 14.8 - - + -
395G MET* 3.4 48.9 - - + +
398G ASP* 3.9 8.1 - - + +
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Residues in contact with LEU 287 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129G GLY 3.8 11.0 - - - +
130G LEU* 4.4 5.6 - - + -
131G VAL* 4.4 13.7 - - + -
135G TYR* 4.3 2.2 - - + -
136G PHE* 4.3 21.3 - - + -
188G ARG* 3.5 37.0 - - - +
286G LEU* 1.3 78.1 - - - +
288G THR* 1.3 64.3 + - - +
289G THR 3.7 0.2 + - - -
301G ALA 3.4 1.4 - - - +
302G LEU* 3.3 8.6 - - - +
303G GLU* 2.8 59.1 + - + +
305G ALA* 4.8 1.1 - - + -
356G TRP* 3.9 33.4 - - + -
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Residues in contact with THR 288 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128G THR 3.8 5.2 - - - +
129G GLY* 3.0 37.9 + - - +
130G LEU* 4.4 2.4 - - - +
194G ILE* 4.2 10.6 - - + +
279G ALA* 4.2 23.6 - - + -
280G VAL 2.5 30.8 + - - +
281G LYS* 4.1 2.1 - - - -
282G SER* 3.8 12.0 + - - -
286G LEU 4.1 0.8 + - - -
287G LEU* 1.3 71.0 - - - +
289G THR* 1.3 65.7 + - - +
300G TYR* 5.0 0.7 - - + -
301G ALA 3.5 10.5 - - - +
302G LEU* 3.9 2.6 - - + +
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Residues in contact with THR 289 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130G LEU* 5.3 2.9 - - - -
187G SER* 3.6 17.4 + - - -
188G ARG* 3.6 25.7 + - - +
194G ILE* 5.1 3.8 - - - -
247G GLN* 3.6 19.5 + - - +
272G LEU* 5.7 1.8 - - + -
287G LEU* 4.7 2.7 - - - -
288G THR* 1.3 78.1 - - - +
290G ILE* 1.3 70.9 + - - +
300G TYR* 3.4 6.4 - - - +
301G ALA* 2.8 45.1 + - + +
303G GLU* 4.2 19.1 - - + +
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Residues in contact with ILE 290 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183G TYR* 4.6 22.0 - - + +
184G THR* 3.1 15.7 - - + +
187G SER* 4.2 13.3 + - - +
192G PHE* 4.7 9.2 - - + -
194G ILE* 3.8 30.1 - - + +
197G LEU* 5.3 4.7 - - + -
220G SER* 5.9 0.4 - - - +
247G GLN* 2.7 30.7 + - - -
289G THR* 1.3 86.5 + - - +
291G ALA* 1.3 72.0 + - - +
298G VAL* 4.1 18.4 - - + -
299G ASN 3.2 9.9 - - - +
300G TYR* 3.9 22.0 - - + -
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Residues in contact with ALA 291 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184G THR* 4.0 6.5 - - - -
247G GLN* 4.0 11.7 - - + +
250G LEU* 4.5 17.7 - - + -
274G ASN* 4.6 3.8 - - - +
289G THR 4.1 0.8 + - - -
290G ILE* 1.3 82.0 - - - +
292G CYS* 1.3 69.9 + - - +
297G GLU 3.7 0.5 - - - +
298G VAL* 3.7 1.7 - - - -
299G ASN* 2.7 34.6 + - + +
300G TYR 4.3 4.3 - - - +
301G ALA* 4.2 18.6 - - + -
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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