Contacts of the strand formed by residues 283 - 290 (chain A) in PDB entry 1W21
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 GLU 283 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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231A ARG* 2.7 42.5 + - - +
249A THR* 4.6 3.6 - - - -
253A ALA* 3.9 2.8 - - - -
281A HIS* 3.5 22.1 + - + +
282A ILE* 1.3 82.1 - - - +
284A GLU* 1.3 74.3 + - + +
285A CYS 3.3 2.6 + - - -
298A CYS* 3.3 3.3 - - - +
299A ARG* 2.7 53.1 + - - +
301A ASN* 4.0 8.8 - - + +
1477A SIA 2.6 36.1 + - - +
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Residues in contact with GLU 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A ARG* 6.5 0.2 - - - -
232A THR 3.8 15.0 + - - +
233A GLN 3.2 17.0 - - - +
234A GLU* 3.9 17.0 - - + +
283A GLU* 1.3 80.4 + - + +
285A CYS* 1.3 66.6 + - - +
286A SER* 3.4 1.2 + - - -
297A ILE 4.3 2.4 - - - +
298A CYS* 4.4 1.7 - - - -
299A ARG* 2.8 32.3 + - + -
357A LYS* 3.0 33.9 + - + +
358A GLY 4.7 0.5 - - - +
412A TYR* 2.3 35.2 + - - -
1477A SIA 3.3 22.7 + - - +
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Residues in contact with CYS 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A THR 5.3 0.2 - - - -
233A GLN* 3.3 29.8 - - + +
235A SER* 3.1 6.6 + - - -
247A VAL* 3.8 17.9 - - + +
282A ILE* 3.6 19.7 - - - -
283A GLU 4.7 0.4 - - - -
284A GLU* 1.3 76.9 - - - +
286A SER* 1.3 58.7 + - - +
287A CYS* 3.9 5.4 - - - -
296A CYS* 3.9 12.8 - - + -
297A ILE 3.7 0.9 - - - -
298A CYS* 2.1 49.6 - - - -
310A ILE* 3.9 4.3 - - - -
357A LYS* 3.1 9.3 + - - -
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Residues in contact with SER 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A SER* 3.5 5.2 - - - -
284A GLU 3.4 0.2 + - - -
285A CYS* 1.3 70.3 - - - +
287A CYS* 1.3 59.9 + - - +
288A TYR* 5.1 1.4 - - - -
295A LYS 3.8 1.2 - - - +
296A CYS* 3.5 0.7 - - - -
297A ILE* 2.8 38.6 + - - +
357A LYS* 2.7 25.3 + - - -
358A GLY 2.7 27.5 + - - -
359A PHE* 3.5 19.0 - - - +
360A ALA 5.4 0.7 - - - +
414A GLY* 3.4 4.0 - - - -
415A ALA* 3.7 14.7 - - - +
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Residues in contact with CYS 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A GLN* 3.6 31.2 - - - +
235A SER* 4.3 3.4 + - - -
236A GLU* 4.2 10.0 + - - +
237A CYS* 5.1 1.3 - - - -
238A VAL* 3.7 21.6 - - + +
245A PRO 6.0 0.7 - - - -
285A CYS* 3.9 5.1 + - - -
286A SER* 1.3 76.0 - - - +
288A TYR* 1.4 65.6 + - - +
294A ILE* 4.2 3.6 - - + -
295A LYS 3.2 4.7 - - - +
296A CYS* 2.1 47.8 - - - -
415A ALA* 3.9 17.2 + - - +
419A TYR* 4.6 0.7 + - - -
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Residues in contact with TYR 288 (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 LEU* 3.8 26.6 - - + +
238A VAL* 3.8 6.5 - - - +
286A SER 5.1 0.9 - - - -
287A CYS* 1.4 76.1 - - - +
289A GLY* 1.3 68.8 + - - +
290A ALA* 4.5 7.4 - - + -
293A VAL 3.8 0.8 - - - +
294A ILE* 3.4 2.5 - - - -
295A LYS* 3.0 64.1 + - + +
297A ILE* 4.5 2.9 - - + -
360A ALA 3.4 23.1 - - - -
361A PHE* 3.6 33.2 - + + -
362A LEU* 2.9 38.4 + - - +
415A ALA* 4.6 7.4 - - + -
416A PHE 5.6 0.4 - - - +
417A ILE* 4.1 5.8 - - + -
419A TYR* 3.2 14.1 - - - +
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Residues in contact with GLY 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A LEU* 4.0 20.6 - - - -
238A VAL* 3.9 3.4 - - - +
288A TYR* 1.3 81.1 - - - +
290A ALA* 1.3 65.5 + - - +
293A VAL 3.3 9.0 - - - -
294A ILE* 4.3 0.9 - - - -
417A ILE* 4.1 3.1 - - - +
419A TYR* 2.8 22.6 + - - -
426A PHE* 3.3 17.6 - - - -
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Residues in contact with ALA 290 (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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93A LEU* 3.9 6.1 - - - +
95A LYS 3.5 12.1 - - - +
96A PRO* 4.4 0.4 - - + -
97A LEU* 3.8 37.5 - - + +
288A TYR* 4.5 5.6 - - + -
289A GLY* 1.3 76.2 - - - +
291A GLY* 1.3 67.1 + - - +
292A GLY 3.1 1.8 - - - -
293A VAL* 3.0 22.8 + - - +
426A PHE* 4.1 1.3 - - + -
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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
------------------------------------------------------------
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