Contacts of the strand formed by residues 280 - 288 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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247A LYS* 3.7 30.5 - - + +
248A GLY 3.4 8.2 + - - +
249A ASN* 3.6 12.8 + - - +
278A ASP* 3.2 11.1 - - + +
279A LYS* 1.3 76.5 - - - +
281A MET* 1.3 73.6 + - - +
282A ILE* 3.9 19.6 + - + +
299A TRP 4.2 3.5 - - - +
300A PHE* 3.7 10.5 - - - -
301A ALA 5.2 0.3 + - - -
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Residues in contact with MET 281 (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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246A ASN 3.8 0.5 - - - +
247A LYS* 3.4 6.4 - - - -
248A GLY 2.6 35.5 + - - +
250A VAL* 3.7 25.6 - - + -
279A LYS 3.4 1.2 + - - -
280A GLU* 1.3 74.6 - - - +
282A ILE* 1.3 64.7 + - - +
283A VAL* 3.9 11.9 - - + -
298A SER* 3.3 26.2 - - - +
299A TRP 3.5 7.4 - - - +
300A PHE* 3.8 12.3 - - + -
345A PHE* 3.7 13.7 - - + -
404A MET* 3.4 26.9 - - + +
407A ARG 4.2 0.9 - - - -
408A ALA* 3.6 28.7 - - - +
411A LEU* 3.9 8.9 - - + +
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Residues in contact with ILE 282 (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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245A ILE* 3.8 31.4 - - + -
246A ASN 3.5 2.7 - - - +
247A LYS* 4.3 12.3 - - + +
280A GLU* 3.9 25.8 - - + +
281A MET* 1.3 77.4 - - - +
283A VAL* 1.3 63.5 + - - +
297A ILE 3.5 1.9 - - - +
298A SER* 3.4 1.7 - - - -
299A TRP* 3.0 51.8 + - + +
532A LEU* 5.4 0.2 - - + -
550A ARG* 6.3 1.1 - - - -
566A THR* 4.3 13.2 - - + -
567A VAL 5.0 3.4 - - - +
568A VAL* 3.6 30.3 - - + -
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Residues in contact with VAL 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A PHE 3.9 0.2 - - - +
245A ILE* 3.4 7.1 - - - +
246A ASN* 3.0 33.1 + - + +
281A MET* 3.9 16.8 - - + -
282A ILE* 1.3 76.7 - - - +
284A LEU* 1.3 70.2 + - - +
285A LYS* 3.9 2.5 + - + +
296A LEU* 4.5 8.5 - - + -
297A ILE 3.3 7.2 - - - +
298A SER* 4.5 5.4 - - - +
408A ALA* 4.1 10.3 - - + +
411A LEU* 3.7 37.9 - - + -
412A TYR* 4.3 32.5 - - + -
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Residues in contact with LEU 284 (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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144A MET* 6.0 4.0 - - + -
243A ILE* 3.6 32.8 - - + -
244A PHE 3.7 6.3 - - - +
245A ILE* 4.1 18.6 - - + -
282A ILE* 3.9 0.6 + - + -
283A VAL* 1.3 73.6 - - - +
285A LYS* 1.3 58.3 + - - +
286A MET* 3.6 10.5 - - + +
296A LEU* 3.1 9.0 - - - +
297A ILE* 2.7 57.1 + - + +
299A TRP* 4.1 14.8 - - + -
419A VAL* 4.6 3.4 - - + -
529A LEU* 5.1 7.9 - - + -
532A LEU* 3.7 33.0 - - + -
534A ILE* 5.8 0.2 - - + -
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Residues in contact with LYS 285 (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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242A LYS 3.9 0.3 - - - +
243A ILE* 3.3 6.6 - - - +
244A PHE* 2.7 57.5 + - + +
283A VAL* 3.9 4.1 + - + +
284A LEU* 1.3 73.0 - - - +
286A MET* 1.3 64.0 + - - +
287A VAL* 3.7 22.4 - - + -
293A ASP* 4.3 2.4 + - - -
412A TYR* 3.2 67.4 + - + +
413A ALA* 4.2 9.9 + - - +
415A ALA* 3.8 22.1 + - + -
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Residues in contact with MET 286 (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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104A ILE* 4.0 28.5 - - + -
106A VAL* 4.4 2.2 - - - -
142A PHE* 3.5 35.9 - - + -
144A MET* 4.7 12.8 - - - +
242A LYS 3.7 2.9 - - - -
243A ILE* 4.1 21.1 - - + -
284A LEU* 3.6 26.5 - - + +
285A LYS* 1.3 79.0 - - - +
287A VAL* 1.3 64.9 + - - +
294A LEU* 2.8 27.2 + - + -
295A GLY 3.0 27.7 + - - +
296A LEU* 3.7 10.1 - - - -
297A ILE* 3.9 10.3 - - + -
412A TYR* 3.8 1.7 + - - -
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Residues in contact with VAL 287 (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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104A ILE* 4.3 0.3 - - - +
241A GLY* 3.2 3.1 - - - -
242A LYS* 2.9 35.5 + - + +
244A PHE* 4.0 26.9 - - + -
285A LYS* 3.7 29.1 - - + -
286A MET* 1.3 79.3 - - - +
288A ASP* 1.3 68.3 + - - +
291A GLY* 4.1 15.0 - - - +
292A ASP 3.3 15.9 - - - +
293A ASP* 3.9 11.9 - - - +
294A LEU* 3.5 10.3 - - - +
412A TYR* 4.1 0.2 - - - +
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Residues in contact with ASP 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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239A LYS* 4.9 17.0 + - + +
240A PRO 3.5 14.6 - - - +
241A GLY* 3.8 2.5 - - - -
242A LYS* 4.8 1.1 + - - +
287A VAL* 1.3 82.2 - - - +
289A LEU* 1.3 59.1 + - - +
290A ASN* 3.5 17.1 + - - +
291A GLY* 2.9 22.5 + - - -
292A ASP* 2.8 46.8 + - - +
294A LEU* 3.6 21.3 - - + +
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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
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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