Contacts of the helix formed by residues 90 - 107 (chain B) in PDB entry 2WZJ
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 ASN 90 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A LYS* 4.6 12.5 + - - +
88B GLN 4.4 0.6 + - - -
89B LEU* 1.3 75.7 - - - +
91B SER* 1.3 61.2 + - - +
92B SER* 3.0 21.2 - - - -
93B SER* 2.5 48.9 + - - -
94B LEU* 3.0 11.7 + - - +
202B PHE 4.8 5.3 + - - -
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Residues in contact with SER 91 (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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170A PHE* 5.6 0.6 - - - -
227A ASP* 4.7 1.8 - - - -
228A GLY* 3.9 18.6 - - - -
229A PRO* 4.0 13.3 - - - +
230A GLU* 5.0 3.5 + - - -
90B ASN* 1.3 73.7 - - - +
92B SER* 1.3 56.9 + - - +
94B LEU* 3.8 13.1 - - - +
95B GLN* 2.9 50.3 + - - +
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Residues in contact with SER 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A ARG* 5.7 0.2 + - - -
225A LYS* 5.5 1.8 - - - -
227A ASP* 3.8 30.5 + - - +
90B ASN* 2.9 15.7 + - - -
91B SER* 1.3 78.7 - - - +
93B SER* 1.3 58.4 + - - +
95B GLN* 3.5 11.4 + - - +
96B LYS* 2.9 27.9 + - - +
99B ARG* 5.1 1.0 + - - -
261C ARG* 5.4 6.0 + - - -
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Residues in contact with SER 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B LEU* 3.8 22.4 - - - -
90B ASN* 2.5 39.4 + - - -
92B SER* 1.3 71.3 - - - +
94B LEU* 1.3 54.9 + - - -
96B LYS* 2.9 7.3 + - - +
97B LEU* 2.6 37.6 + - - +
202B PHE* 4.0 27.6 + - - +
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Residues in contact with LEU 94 (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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170A PHE* 3.8 31.0 - - + -
86B LYS* 4.2 35.4 - - + +
89B LEU* 3.9 31.2 - - + +
90B ASN 3.0 7.6 + - - +
91B SER* 3.8 16.2 - - - +
93B SER* 1.3 76.9 - - - +
95B GLN* 1.3 63.2 + - - +
97B LEU* 3.6 5.8 - - + +
98B PHE* 3.0 49.6 + - + -
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Residues in contact with GLN 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A PHE* 3.0 36.5 - - + +
172A VAL* 3.5 16.5 - - + +
174A ARG* 2.9 28.6 + - - -
227A ASP 3.0 23.9 + - - -
228A GLY* 4.2 1.4 - - - -
229A PRO* 4.5 2.0 - - - +
91B SER* 2.9 35.5 + - - +
92B SER* 3.6 8.8 + - - +
94B LEU* 1.3 76.3 - - - +
96B LYS* 1.3 63.6 + - - +
98B PHE* 3.5 1.2 + - - +
99B ARG* 3.0 38.4 + - - +
102B ARG* 5.0 1.4 + - - -
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Residues in contact with LYS 96 (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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92B SER 2.9 18.0 + - - +
93B SER* 2.9 6.9 + - - +
95B GLN* 1.3 76.1 - - - +
97B LEU* 1.3 65.3 + - - +
99B ARG* 3.1 29.8 + - - +
100B GLU* 2.9 48.6 + - - +
200B PHE* 4.9 4.5 - - + -
202B PHE* 4.9 11.4 - - + -
253C GLN* 4.0 10.1 - - - +
257C GLU* 3.2 38.9 + - - +
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Residues in contact with LEU 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B ILE* 3.8 40.8 - - + -
86B LYS* 5.4 2.2 - - + -
89B LEU* 4.1 13.0 - - + -
93B SER 2.6 20.2 + - - +
94B LEU* 3.6 10.1 - - + +
96B LYS* 1.3 72.4 - - - +
98B PHE* 1.3 69.8 + - + +
100B GLU* 3.2 8.9 + - - +
101B VAL* 2.9 29.2 + - + +
125B LEU* 3.9 29.2 - - + -
127B LEU* 4.8 0.2 - - + -
196B PHE* 4.0 12.8 - - + -
202B PHE* 3.9 18.7 - - + -
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Residues in contact with PHE 98 (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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169A LYS* 4.3 3.6 - - - +
170A PHE* 3.2 38.8 - + + -
86B LYS* 4.8 5.4 - - + -
94B LEU* 3.0 41.5 + - + +
95B GLN 4.2 1.3 - - - +
97B LEU* 1.3 81.5 - - + +
99B ARG* 1.3 66.9 + - - +
100B GLU 3.0 1.8 - - - -
101B VAL* 3.3 15.5 + - + +
102B ARG* 3.0 44.0 + - - +
120B GLU* 3.4 37.5 - - - -
125B LEU* 4.4 21.5 - - + -
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Residues in contact with ARG 99 (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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99A ARG* 4.2 31.8 - - + +
102A ARG* 6.0 1.8 - - - +
103A ILE* 4.8 14.8 - - + -
170A PHE 5.5 1.0 + - - -
92B SER 5.1 1.2 + - - -
95B GLN* 3.0 40.3 + - - +
96B LYS* 3.1 41.0 + - + +
98B PHE* 1.3 76.2 - - - +
100B GLU* 1.3 63.7 + - + +
102B ARG* 3.5 26.9 + - - +
103B ILE* 3.4 28.7 + - + +
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Residues in contact with GLU 100 (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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96B LYS* 2.9 41.8 + - - +
97B LEU* 3.4 10.6 - - - +
98B PHE 3.0 0.2 - - - -
99B ARG* 1.3 77.5 - - + +
101B VAL* 1.3 66.1 + - - +
102B ARG 3.0 1.3 - - - -
103B ILE* 3.0 23.1 + - + +
104B MET* 3.1 12.8 + - - +
195B GLY* 3.2 24.2 - - - +
196B PHE* 3.8 22.9 - - + +
202B PHE* 4.7 4.3 - - - -
253C GLN* 2.8 36.9 + - - +
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Residues in contact with VAL 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B LEU* 2.9 22.1 + - + +
98B PHE* 3.3 16.5 + - + +
100B GLU* 1.3 74.9 - - - +
102B ARG* 1.3 62.9 + - + +
104B MET* 3.4 12.7 + - + +
105B LYS* 3.2 41.1 + - + +
115B LEU* 4.4 3.0 - - + +
118B VAL* 4.4 18.4 - - + -
125B LEU* 4.3 11.9 - - + -
127B LEU* 3.7 37.0 - - + -
196B PHE* 4.7 0.8 - - + +
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Residues in contact with ARG 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A ARG* 5.7 3.7 + - - -
103A ILE* 4.4 14.5 - - - +
106A VAL* 4.1 31.1 - - + +
169A LYS* 3.1 30.9 + - - +
170A PHE 4.7 2.4 + - - -
171A ILE* 3.5 25.3 - - - +
95B GLN 5.0 0.4 + - - -
98B PHE* 3.0 24.2 + - + +
99B ARG* 3.6 42.9 + - - +
100B GLU 3.0 0.6 - - - -
101B VAL* 1.3 79.0 - - + +
103B ILE* 1.3 64.6 + - + +
105B LYS* 3.3 23.4 + - + +
106B VAL* 3.5 12.6 + - - +
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Residues in contact with ILE 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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99A ARG* 6.6 0.2 - - - -
102A ARG* 3.9 34.5 - - - +
99B ARG* 3.4 17.4 + - + +
100B GLU* 3.0 18.5 + - + +
102B ARG* 1.3 76.3 - - + +
104B MET* 1.3 67.5 + - - +
106B VAL* 3.0 25.9 + - - +
107B LEU* 3.3 24.1 + - + +
171B ILE* 4.4 21.1 - - + -
194B PHE 4.1 5.2 - - - +
195B GLY* 3.7 20.6 - - - -
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Residues in contact with MET 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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100B GLU 3.1 3.6 + - - +
101B VAL* 3.7 16.2 - - + +
103B ILE* 1.3 79.6 - - - +
105B LYS* 1.3 61.1 + - - +
106B VAL 3.6 0.2 + - - -
107B LEU* 4.0 20.2 + - + +
113B VAL* 5.4 11.9 - - - +
114B LYS* 5.0 1.1 + - - -
115B LEU* 4.0 34.1 + - + +
127B LEU* 4.2 9.4 - - + -
129B MET* 3.7 24.7 - - + -
194B PHE* 6.2 0.2 - - + -
195B GLY* 4.3 18.8 - - - +
196B PHE* 3.1 52.9 - - + +
351B TYR* 4.6 1.6 + - - -
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Residues in contact with LYS 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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101B VAL* 3.2 25.4 + - + +
102B ARG* 3.7 19.7 - - + +
103B ILE 3.1 1.6 + - - -
104B MET* 1.3 77.4 - - - +
106B VAL* 1.3 60.9 + - - +
107B LEU 4.7 0.6 - - - +
114B LYS* 4.6 2.8 + - - -
115B LEU* 3.8 9.0 - - + -
118B VAL* 4.2 17.3 - - - +
349B GLN* 5.1 6.8 + - - +
350B ARG 4.7 7.1 + - - -
351B TYR* 3.2 61.5 + - + -
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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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102A ARG* 5.0 12.6 - - + -
105A LYS* 6.3 0.9 - - - +
102B ARG 3.5 7.5 + - - +
103B ILE* 3.0 29.6 + - - +
105B LYS* 1.3 78.8 - - - +
107B LEU* 1.3 68.8 + - + +
108B ASN* 4.6 0.7 - - - +
165B TYR* 3.8 2.4 + - - -
169B LYS* 3.7 21.8 + - + +
171B ILE* 4.5 13.0 - - + -
318B GLU* 3.3 18.8 - - - +
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Residues in contact with LEU 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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103B ILE* 3.3 29.7 + - + +
104B MET* 4.0 16.5 + - + +
105B LYS 3.6 0.8 - - - -
106B VAL* 1.3 74.7 - - - +
108B ASN* 1.3 61.0 + - - +
109B HIS 3.9 1.7 + - - -
112B ILE* 4.2 19.9 - - + +
114B LYS* 4.1 17.2 + - - +
165B TYR* 3.8 16.6 - - + -
166B CYS* 3.8 25.1 - - - -
169B LYS* 4.4 9.2 - - + -
171B ILE* 3.8 20.9 - - + -
194B PHE* 4.0 27.8 - - + -
195B GLY 5.1 0.7 - - - +
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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
------------------------------------------------------------
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