Contacts of the helix formed by residues 287 - 296 (chain B) in PDB entry 4XHS
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 THR 287 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89B LYS* 5.9 4.0 - - - +
282B GLU 4.2 3.1 - - - +
283B ASN* 3.5 31.4 - - - +
284B TYR 2.9 15.6 + - - +
285B LEU 2.8 5.1 + - - +
286B LEU* 1.3 79.6 - - - +
288B ASP* 1.3 65.1 + - - +
289B GLU* 3.3 22.4 + - - +
290B GLY 3.0 10.9 + - - -
291B LEU* 3.0 23.9 + - - +
305B LEU* 3.4 9.0 - - - -
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Residues in contact with ASP 288 (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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287B THR* 1.3 73.5 - - - +
289B GLU* 1.3 67.5 + - + +
291B LEU* 4.0 1.0 - - - +
292B GLU* 3.0 31.5 + - - +
305B LEU* 3.6 2.9 - - - +
307B SER* 2.7 34.2 + - - +
308B TYR* 3.5 32.2 + - + +
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Residues in contact with GLU 289 (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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27B LYS* 5.5 8.7 + - - +
287B THR* 3.3 19.9 + - - +
288B ASP* 1.3 90.3 + - + +
290B GLY* 1.3 64.2 + - - +
292B GLU* 3.6 10.6 + - - +
293B ALA* 3.1 22.9 + - - +
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Residues in contact with GLY 290 (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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24B VAL* 3.5 21.4 - - - +
284B TYR 3.4 21.8 - - - -
285B LEU* 3.5 8.3 - - - -
287B THR* 3.0 9.9 + - - -
289B GLU* 1.3 75.2 - - - +
291B LEU* 1.3 64.8 + - - +
293B ALA* 3.2 12.6 + - - +
294B VAL* 3.3 12.5 + - - +
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Residues in contact with LEU 291 (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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109B ILE* 4.0 23.6 - - + +
285B LEU* 3.3 34.1 + - + +
286B LEU* 4.3 11.7 - - + -
287B THR 3.0 12.5 + - - +
290B GLY* 1.3 72.2 - - - +
292B GLU* 1.3 60.8 + - - +
294B VAL* 3.3 3.7 + - + +
295B ASN* 2.8 31.4 + - - +
300B LEU* 3.9 13.0 - - + +
303B VAL* 3.9 22.2 - - + -
305B LEU* 3.6 36.8 - - + +
308B TYR* 3.7 16.2 - - + -
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Residues in contact with GLU 292 (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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288B ASP 3.0 20.8 + - - +
289B GLU* 3.8 8.6 - - - +
290B GLY 3.3 0.2 - - - -
291B LEU* 1.3 76.3 - - - +
293B ALA* 1.3 56.6 + - - +
295B ASN 3.8 0.2 - - - -
296B LYS* 2.9 70.3 + - + +
308B TYR* 3.5 28.1 - - + +
311B GLU* 5.4 3.6 - - - +
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Residues in contact with ALA 293 (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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20B GLY* 3.4 20.4 - - - +
23B GLU* 4.2 19.7 - - + +
24B VAL* 3.9 16.8 - - + +
289B GLU 3.1 14.6 + - - +
290B GLY 3.2 9.6 + - - +
292B GLU* 1.3 78.6 - - - +
294B VAL* 1.3 61.4 + - - +
296B LYS* 3.7 6.1 + - - +
297B ASP* 3.6 9.2 + - - +
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Residues in contact with VAL 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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12B ILE* 5.8 4.9 - - + -
17B GLY* 3.8 20.8 - - - +
20B GLY* 4.0 6.7 - - - +
21B LEU* 3.8 30.7 - - + +
24B VAL* 4.3 1.1 - - + -
285B LEU* 3.9 19.3 - - + -
290B GLY 3.3 12.3 + - - +
291B LEU 3.3 6.4 + - - +
292B GLU 3.3 0.4 - - - -
293B ALA* 1.3 73.8 - - - +
295B ASN* 1.3 66.6 + - - +
297B ASP* 3.0 14.0 + - - +
298B LYS 3.1 14.7 + - - +
300B LEU* 3.8 30.1 - - + -
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Residues in contact with ASN 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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291B LEU 2.8 17.8 + - - +
292B GLU 3.8 1.8 - - - +
294B VAL* 1.3 78.3 - - - +
296B LYS* 1.3 61.5 + - + +
298B LYS* 3.3 21.2 - - - -
299B PRO* 3.4 15.7 - - - +
300B LEU* 2.9 35.2 + - + +
301B GLY 4.3 2.8 + - - +
308B TYR* 3.6 22.7 + - + +
312B LEU* 4.2 24.2 - - - +
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Residues in contact with LYS 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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292B GLU* 2.9 54.8 + - + +
293B ALA* 4.1 6.3 - - - +
294B VAL 3.2 0.2 - - - -
295B ASN* 1.3 77.2 - - + +
297B ASP* 1.3 55.2 + - - +
308B TYR* 5.5 0.2 - - - +
504B NA 2.5 23.1 - - - -
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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