Contacts of the strand formed by residues 102 - 110 (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 TYR 102 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99B PHE* 3.6 3.3 - - - -
101B GLY* 1.3 78.3 - - - -
103B HIS* 1.3 65.8 + - - +
104B ILE* 4.2 10.3 - - + -
144B MET* 5.0 1.8 - - + -
145B ALA 3.4 17.3 - - - +
146B GLU* 4.7 7.2 - - - -
147B PRO* 5.4 0.9 - - + -
240B PRO* 3.7 1.0 - - - +
241B GLY 3.1 32.7 + - - +
242B LYS* 5.4 0.4 - - - -
243B ILE* 3.6 33.7 - - + -
419B VAL* 3.2 23.7 + - + -
420B THR* 3.2 8.9 + - + -
421B GLY 2.7 43.4 + - - -
423B LEU* 3.5 29.8 - - + -
529B LEU 4.1 1.6 - - - -
530B GLY* 3.7 11.2 + - - -
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Residues in contact with HIS 103 (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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290A ASN 5.0 4.5 - - - -
291A GLY* 6.1 1.6 - - - -
99B PHE* 5.3 4.9 + + - -
101B GLY 3.9 0.4 + - - -
102B TYR* 1.3 73.1 - - - +
104B ILE* 1.3 60.7 + - - +
144B MET* 3.4 6.1 - - - -
145B ALA* 2.9 34.8 + - + +
146B GLU 3.7 10.8 - - - -
147B PRO* 3.0 32.2 + - + +
148B ASP 5.1 0.2 - - - -
149B GLY* 4.5 7.0 - - - -
238B MET* 3.5 24.3 - - + +
239B LYS* 3.3 3.8 - - - +
240B PRO* 3.5 39.5 - - + +
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Residues in contact with ILE 104 (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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102B TYR* 4.2 14.1 - - + +
103B HIS* 1.3 79.7 - - - +
105B GLY* 1.3 68.6 + - - +
106B VAL* 4.5 2.9 - - + -
143B ILE 3.3 6.1 - - - +
144B MET* 4.5 7.9 - - + -
237B ASN 3.8 1.9 - - - +
238B MET* 3.3 2.5 - - - -
239B LYS* 2.6 42.7 + - - +
241B GLY* 4.0 2.7 - - - -
242B LYS 3.4 37.5 - - - +
243B ILE* 3.6 19.7 - - + -
286B MET* 4.1 32.5 - - + -
287B VAL 4.3 5.4 - - - +
294B LEU* 4.2 15.7 - - + +
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Residues in contact with GLY 105 (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* 1.3 75.3 - - - +
106B VAL* 1.3 67.8 + - - +
142B PHE* 3.5 0.7 - - - -
143B ILE* 2.8 38.4 + - - -
234B ALA* 3.4 25.7 - - - +
237B ASN 3.9 7.9 - - - -
238B MET* 3.9 4.9 - - - +
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Residues in contact with VAL 106 (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* 4.5 13.7 - - + -
105B GLY* 1.3 79.3 - - - +
107B GLY* 1.3 59.5 + - - +
141B ALA 3.4 6.5 - - - +
142B PHE* 3.6 24.5 - - + -
233B ILE* 3.7 8.1 - - - +
234B ALA* 3.4 17.3 + - - +
237B ASN* 4.6 8.0 + - + +
286B MET* 4.6 3.8 - - - -
294B LEU* 3.5 38.6 - - + +
340B PRO 4.0 7.0 - - - +
342B VAL* 4.0 18.6 - - + +
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Residues in contact with GLY 107 (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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106B VAL* 1.3 77.0 - - - +
108B ARG* 1.3 61.2 + - - +
139B SER 3.7 0.3 - - - +
140B ARG* 3.3 4.0 - - - -
141B ALA 2.9 34.3 + - - +
230B SER* 3.6 20.8 - - - -
233B ILE* 3.7 11.9 - - - -
234B ALA* 3.7 0.6 - - - +
342B VAL* 3.9 10.4 - - - +
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Residues in contact with ARG 108 (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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107B GLY* 1.3 75.6 - - - +
109B ALA* 1.3 64.8 + - - +
138B TYR* 3.7 30.3 - - + -
139B SER 3.3 4.0 - - - -
140B ARG* 3.8 19.1 - - + +
229B LYS* 5.9 0.2 - - - -
233B ILE* 3.4 19.4 - - - +
327B GLU* 3.0 38.1 + - - -
331B ASN* 4.4 0.4 - - - +
337B GLY* 3.2 24.5 + - - +
338B GLN* 3.1 25.1 + - - +
339B GLY 2.8 23.8 + - - +
341B PHE 3.1 19.6 + - - -
342B VAL* 3.7 10.3 - - + +
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Residues in contact with ALA 109 (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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108B ARG* 1.3 77.2 - - - +
110B ASP* 1.3 61.3 + - - +
138B TYR* 3.3 7.7 - - - -
139B SER* 2.8 37.9 + - - -
226B GLY* 3.3 25.1 - - - +
229B LYS* 3.9 24.0 - - + +
230B SER* 3.5 15.9 - - - +
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Residues in contact with ASP 110 (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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109B ALA* 1.3 71.2 - - - +
111B CYS* 1.3 58.6 + - - +
112B THR* 2.6 35.3 + - - -
136B ARG* 3.0 34.5 + - - +
137B LEU 3.1 6.0 - - - +
138B TYR* 4.1 12.2 - - + -
222B HIS* 3.6 22.0 + - + -
226B GLY* 3.5 15.9 - - - -
229B LYS* 5.7 1.7 - - - +
690B HIS 4.8 3.6 - - - +
691B GLN* 5.1 2.9 - - - +
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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