Contacts of the strand formed by residues 294 - 298 (chain B) in PDB entry 4NSW
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 294 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289B THR 3.4 3.1 - - - +
290B ILE* 3.5 5.2 - - - +
291B GLN 3.0 32.4 + - - +
292B SER* 3.9 13.9 + - - +
293B ASN* 1.3 78.8 - - - +
295B LEU* 1.3 59.7 - - - +
296B VAL* 3.9 21.0 - - + +
305B VAL* 5.8 2.2 - - - +
307B VAL* 4.3 14.8 - - - +
309B VAL 3.5 8.7 - - - +
310B ASP* 3.4 25.4 - - - +
312B LEU* 4.6 4.7 - - - -
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Residues in contact with LEU 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B LEU* 6.0 0.4 - - + -
288B PHE* 3.9 22.0 - - + -
289B THR 3.7 15.0 - - - +
290B ILE* 3.7 22.7 - - + -
294B GLN* 1.3 71.9 - - - +
296B VAL* 1.3 62.1 + - - +
307B VAL* 3.8 0.3 - - - -
308B VAL* 2.9 40.2 + - + +
309B VAL* 3.2 24.5 + - + +
312B LEU* 3.9 17.4 - - + +
331B VAL* 4.3 13.7 - - + -
338B CYS* 4.7 2.5 - - - -
340B LEU* 3.8 29.2 - - + -
351B TRP* 4.8 5.4 - - + -
355B VAL* 5.6 6.3 - - + -
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Residues in contact with VAL 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B PHE* 3.1 10.1 - - - -
289B THR* 2.7 61.0 + - + +
291B GLN* 6.2 1.1 - - + -
294B GLN* 4.1 20.2 - - + +
295B LEU* 1.3 78.4 - - - +
297B TYR* 1.3 60.9 + - - +
298B GLN* 5.8 1.6 - - - +
305B VAL* 3.9 32.3 - - + -
306B THR 3.2 9.2 - - - +
307B VAL* 3.9 22.2 - - + -
308B VAL* 4.1 1.3 - - - -
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Residues in contact with TYR 297 (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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274B LYS* 3.5 29.4 - - + +
286B ARG* 3.4 40.4 - - + -
287B TRP 3.0 13.0 - - - +
288B PHE* 3.8 31.4 - + + -
296B VAL* 1.3 76.1 - - - +
298B GLN* 1.3 72.4 + - - +
299B LYS* 5.4 2.2 - - + -
304B PRO 4.4 0.2 - - - +
305B VAL* 3.6 1.4 - - - -
306B THR* 3.0 72.0 + - + +
308B VAL* 4.1 8.1 - - + -
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Residues in contact with GLN 298 (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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15A PRO* 5.8 1.7 - - + +
286B ARG* 3.9 3.3 - - - +
287B TRP* 2.9 52.5 + - + +
289B THR* 4.7 5.7 + - - -
296B VAL* 5.8 1.8 - - + +
297B TYR* 1.3 85.5 - - - +
299B LYS* 1.3 62.5 + - - +
300B LYS 3.8 13.0 - - - +
301B TYR* 4.7 1.9 - - - +
302B LYS* 4.0 10.3 - - - +
303B ASP* 2.8 43.2 + - + +
304B PRO 5.0 1.3 - - - -
305B VAL* 4.1 19.8 - - + +
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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
------------------------------------------------------------
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