Contacts of the strand formed by residues 280 - 288 (chain B) in PDB entry 4WGK
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 280 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247B LYS* 3.6 32.0 + - + +
248B GLY* 3.4 9.3 + - - +
249B ASN* 3.6 12.2 + - - +
278B ASP* 3.2 10.5 - - + +
279B LYS* 1.3 76.9 - - - +
281B MET* 1.3 71.7 + - - +
282B ILE* 3.8 20.1 + - + +
299B TRP 4.1 3.3 - - - +
300B PHE* 3.8 9.7 - - - -
301B ALA 5.2 0.3 + - - -
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Residues in contact with MET 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B ASN 3.9 0.3 - - - +
247B LYS* 3.3 5.7 - - - -
248B GLY 2.7 35.7 + - - +
250B VAL* 3.7 26.2 - - + -
279B LYS 3.3 1.4 + - - -
280B GLU* 1.3 75.4 - - - +
282B ILE* 1.3 64.8 + - - +
283B VAL* 4.0 11.0 - - + -
298B SER* 3.3 20.2 - - - +
299B TRP 3.5 8.1 - - - +
300B PHE* 3.9 13.7 - - + -
345B PHE* 3.7 21.3 - - + -
404B MET* 3.5 24.2 - - + +
407B ARG 4.2 0.7 - - - -
408B ALA* 3.6 29.4 - - - +
411B LEU* 3.9 8.4 - - + +
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Residues in contact with ILE 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B ILE* 4.0 29.4 - - + -
246B ASN 3.6 2.9 - - - +
247B LYS* 4.0 15.0 - - + -
280B GLU* 3.8 22.4 + - + +
281B MET* 1.3 76.0 - - - +
283B VAL* 1.3 63.9 + - - +
284B LEU* 5.9 0.7 - - + -
297B ILE 3.5 1.9 - - - +
298B SER* 3.5 1.6 - - - -
299B TRP* 3.0 48.4 + - + +
532B LEU* 5.3 0.7 - - + -
550B ARG* 6.3 1.8 - - - +
566B THR* 4.1 15.0 - - + -
567B VAL 4.9 3.4 - - - +
568B VAL* 3.6 34.1 - - + -
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Residues in contact with VAL 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B ILE* 3.5 6.8 - - - +
246B ASN* 3.0 33.0 + - + +
281B MET* 4.0 23.6 - - + -
282B ILE* 1.3 75.7 - - - +
284B LEU* 1.3 70.0 + - - +
285B LYS* 3.9 2.7 + - + +
296B LEU* 4.4 8.3 - - + -
297B ILE 3.3 6.7 - - - +
298B SER* 4.4 6.3 - - - +
408B ALA* 4.0 10.3 - - + +
411B LEU* 3.8 27.8 - - + -
412B TYR* 4.3 31.9 - - + +
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Residues in contact with LEU 284 (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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144B MET* 6.0 0.4 - - - -
243B ILE* 3.6 29.8 - - + -
244B PHE 3.6 7.2 - - - +
245B ILE* 4.1 19.5 - - + -
282B ILE 4.0 0.4 + - - -
283B VAL* 1.3 73.3 - - - +
285B LYS* 1.3 60.1 + - - +
286B MET* 3.7 10.8 - - + +
296B LEU* 3.1 8.0 - - - -
297B ILE* 2.7 52.9 + - + +
299B TRP* 4.1 13.9 - - + -
419B VAL* 4.4 4.0 - - + -
529B LEU* 4.0 17.7 - - + -
532B LEU* 3.7 34.1 - - + -
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Residues in contact with LYS 285 (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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242B LYS 3.9 0.5 - - - +
243B ILE* 3.3 5.9 - - - +
244B PHE* 2.7 58.5 + - + +
283B VAL* 3.9 3.7 + - + +
284B LEU* 1.3 73.2 - - - +
286B MET* 1.3 64.1 + - - +
287B VAL* 3.7 22.4 - - + -
293B ASP* 4.3 3.2 + - - -
412B TYR* 3.3 68.3 + - + +
413B ALA* 4.3 10.1 + - - +
415B ALA* 4.0 21.0 + - + +
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Residues in contact with MET 286 (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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104B ILE* 4.1 28.7 - - + -
106B VAL* 4.6 1.6 - - - -
142B PHE* 3.5 35.0 - - + -
144B MET* 4.5 13.5 - - - +
242B LYS 3.7 3.1 - - - -
243B ILE* 4.2 21.1 - - + -
284B LEU* 3.7 12.1 - - + +
285B LYS* 1.3 78.8 - - - +
287B VAL* 1.3 64.7 + - - +
294B LEU* 2.9 25.7 + - + -
295B GLY 3.0 20.9 + - - +
296B LEU* 3.6 28.5 - - - -
297B ILE* 3.8 14.1 - - + -
412B TYR* 4.0 1.4 + - - -
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Residues in contact with VAL 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B ILE* 4.3 0.5 - - - +
241B GLY* 3.2 3.5 - - - -
242B LYS* 2.9 36.3 + - + +
244B PHE* 3.9 26.9 - - + -
285B LYS* 3.7 29.1 - - + -
286B MET* 1.3 78.6 - - - +
288B ASP* 1.3 68.6 + - - +
291B GLY* 4.4 11.2 - - - +
292B ASP 3.2 18.2 - - - +
293B ASP* 3.9 10.8 - - - +
294B LEU* 3.6 9.3 - - - +
412B TYR* 4.2 0.7 - - - +
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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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239B LYS* 4.6 16.7 + - + +
240B PRO 3.5 14.4 - - - +
241B GLY* 3.9 2.9 - - - -
242B LYS* 5.6 1.4 - - - +
287B VAL* 1.3 82.2 - - - +
289B LEU* 1.3 61.3 + - - +
290B ASN* 3.3 18.7 + - - +
291B GLY* 3.0 21.0 + - - -
292B ASP* 2.7 50.8 + - - +
294B LEU* 3.6 20.7 - - + +
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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