Contacts of the strand formed by residues 239 - 249 (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 LYS 239 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103A HIS* 3.7 4.9 - - - -
104A ILE* 2.8 34.1 + - - +
237A ASN* 4.0 16.6 - - - +
238A MET* 1.3 80.9 - - - +
240A PRO* 1.3 80.2 - - + +
241A GLY 3.4 0.7 + - - -
288A ASP* 4.9 16.0 + - + +
294A LEU* 4.4 25.0 - - + +
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Residues in contact with PRO 240 (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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102A TYR 3.7 3.4 - - - +
103A HIS* 3.5 30.7 - - + +
238A MET 4.8 0.7 - - - +
239A LYS* 1.3 87.5 - - + +
241A GLY* 1.3 58.1 + - - +
288A ASP* 3.5 8.5 - - - +
289A LEU* 3.3 41.1 + - + +
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Residues in contact with GLY 241 (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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101A GLY* 4.0 3.3 - - - -
102A TYR* 3.0 32.7 + - - +
104A ILE* 4.0 7.9 - - - -
239A LYS 3.4 2.6 + - - -
240A PRO* 1.3 74.6 - - - +
242A LYS* 1.3 67.1 + - - +
287A VAL 3.2 14.4 - - - -
288A ASP* 3.8 2.0 - - - -
289A LEU* 3.8 13.0 - - - +
294A LEU* 5.2 0.7 - - - -
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Residues in contact with LYS 242 (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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101A GLY* 5.5 5.8 - - - -
102A TYR* 5.2 2.7 - - - -
104A ILE* 3.5 5.6 - - - +
241A GLY* 1.3 78.9 - - - +
243A ILE* 1.3 66.1 + - - +
244A PHE* 3.8 26.1 + - + -
285A LYS 3.9 0.3 - - - +
286A MET* 3.7 0.7 - - - -
287A VAL* 2.9 36.1 + - + +
288A ASP 4.8 1.3 - - - +
289A LEU* 4.3 18.2 - - + -
418A GLU* 3.2 34.9 + - - +
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Residues in contact with ILE 243 (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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102A TYR* 3.6 26.8 - - + -
104A ILE* 3.6 17.5 - - + -
144A MET* 3.7 30.5 - - + -
242A LYS* 1.3 78.4 - - - +
244A PHE* 1.3 60.6 + - - +
284A LEU* 3.6 36.3 - - + -
285A LYS 3.3 8.1 - - - +
286A MET* 4.1 7.6 - - + -
418A GLU* 3.5 5.5 - - - +
419A VAL* 2.6 52.6 + - + +
529A LEU* 5.1 11.7 - - + -
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Residues in contact with PHE 244 (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* 3.8 35.4 - - + -
243A ILE* 1.3 75.5 - - - +
245A ILE* 1.3 60.5 + - - +
284A LEU* 3.5 6.1 - - - +
285A LYS* 2.7 61.2 + - + -
287A VAL* 4.0 20.0 - - + -
415A ALA* 4.1 14.8 - - + -
416A SER* 3.3 33.0 - - - -
417A GLN 3.3 5.2 - - - +
418A GLU* 3.5 25.4 - - + -
419A VAL* 4.3 2.7 - - - +
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Residues in contact with ILE 245 (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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244A PHE* 1.3 75.4 - - - +
246A ASN* 1.3 68.1 + - - +
247A LYS* 3.8 26.2 - - - +
282A ILE* 3.8 21.1 - - + -
283A VAL 3.4 12.1 - - - +
284A LEU* 4.1 11.2 - - + -
415A ALA* 4.6 3.5 - - - +
417A GLN* 2.9 45.7 + - + +
419A VAL* 3.7 19.7 - - + -
531A SER* 6.0 0.7 - - - +
532A LEU* 4.2 17.7 - - + -
566A THR* 4.1 15.3 - - + +
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Residues in contact with ASN 246 (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* 1.3 78.1 - - - +
247A LYS* 1.3 87.0 + - - +
281A MET 3.8 0.2 - - - +
282A ILE* 3.5 4.9 - - - +
283A VAL* 3.0 34.9 + - + +
411A LEU* 2.9 46.8 + - + +
414A SER* 3.1 24.0 + - - -
415A ALA* 3.5 16.2 - - + +
416A SER 5.3 0.7 - - - -
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Residues in contact with LYS 247 (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 19.5 - - + +
246A ASN* 1.3 92.4 + - - +
248A GLY* 1.3 58.8 + - - +
280A GLU* 3.7 29.8 - - - +
281A MET 3.4 7.9 - - - +
282A ILE* 4.3 9.1 - - + +
411A LEU* 3.4 12.8 - - - +
566A THR* 3.2 40.9 + - - +
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Residues in contact with GLY 248 (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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247A LYS* 1.3 75.7 - - - +
249A ASN* 1.3 61.7 + - - -
280A GLU* 3.4 3.8 - - - +
281A MET* 2.6 43.3 + - - +
407A ARG* 3.3 19.7 - - - -
411A LEU* 3.7 5.8 - - - +
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Residues in contact with ASN 249 (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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248A GLY* 1.3 73.7 - - - -
250A VAL* 1.3 57.8 + - - +
251A ASP* 4.1 13.9 + - - +
279A LYS* 3.4 17.4 - - + +
280A GLU* 3.6 22.3 + - - +
407A ARG* 2.6 34.1 + - - +
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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