Contacts of the helix formed by residues 97 - 109 (chain B) in PDB entry 1W98
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 97 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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278A LYS* 3.0 33.8 + - - +
93B LEU* 4.1 0.9 - - - -
96B ALA* 1.3 75.2 - - - +
98B ARG* 1.3 53.1 + - - +
99B GLU* 2.5 41.9 + - - +
100B GLU* 3.0 37.6 + - - +
101B VAL* 2.7 34.5 + - - +
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Residues in contact with ARG 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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88B SER* 3.2 32.4 + - - +
90B LEU* 2.9 28.8 + - + +
91B PRO* 3.1 27.3 - - - +
92B VAL* 3.5 30.8 - - - +
93B LEU* 3.2 22.3 - - + +
96B ALA 3.6 4.9 + - - -
97B ASN* 1.3 73.4 + - - +
99B GLU* 1.3 77.7 + - + +
101B VAL* 4.1 0.3 - - - +
102B TRP* 3.0 32.4 + - - +
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Residues in contact with GLU 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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296A LEU 5.7 1.2 - - - +
97B ASN* 2.5 30.3 + - - +
98B ARG* 1.3 97.3 + - + +
100B GLU* 1.3 58.2 + - - +
102B TRP* 4.0 3.9 - - - +
103B LYS* 3.0 32.8 + - - +
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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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116A ALA 5.1 0.9 - - - +
117A PHE* 5.2 7.8 - - - -
120A SER* 3.3 26.3 + - - -
121A HIS* 5.4 0.3 - - - -
278A LYS* 4.6 8.7 - - - +
97B ASN* 3.0 37.1 + - + +
99B GLU* 1.3 77.2 - - - +
101B VAL* 1.3 65.8 + - - +
103B LYS* 3.3 10.5 + - + +
104B ILE* 3.0 42.1 + - + +
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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
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120A SER* 3.8 24.3 - - - +
122A ARG* 4.3 16.8 - - + -
154A VAL* 5.7 0.9 - - + -
90B LEU* 4.2 6.7 - - + -
93B LEU* 3.6 27.8 - - + -
95B TRP* 4.0 12.3 - - + +
96B ALA* 3.6 20.9 - - + -
97B ASN 2.7 22.7 + - - +
98B ARG 4.1 0.4 - - - +
100B GLU* 1.3 71.4 - - - +
102B TRP* 1.3 64.7 + - - +
104B ILE* 3.3 3.3 + - - +
105B MET* 3.0 42.4 + - - +
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Residues in contact with TRP 102 (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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88B SER* 3.3 24.3 - - - +
89B PRO* 3.4 32.5 - - + -
90B LEU* 3.9 25.4 - - + -
98B ARG 3.0 21.1 + - - +
99B GLU* 4.0 4.0 - - - +
101B VAL* 1.3 76.6 - - - +
103B LYS* 1.3 53.7 - - - +
105B MET* 3.2 12.8 + - + +
106B LEU* 2.8 68.6 + - + +
234B TRP* 3.3 33.9 - + - -
237B VAL* 4.6 12.3 - - + -
238B TYR* 4.7 7.9 - + - -
302B SER* 4.7 0.4 - - - -
303B GLY* 4.3 11.6 - - - -
304B TYR* 4.7 11.0 - + - -
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Residues in contact with LYS 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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99B GLU 3.0 17.7 + - - +
100B GLU* 3.3 16.8 - - + +
102B TRP* 1.3 77.6 - - + +
104B ILE* 1.3 80.4 + - + +
106B LEU* 3.3 10.8 + - - +
107B ASN* 2.8 54.6 + - - +
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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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120A SER* 3.6 24.5 - - - +
121A HIS* 3.5 59.9 - - + +
122A ARG* 6.2 1.3 - - - +
100B GLU* 3.0 35.6 + - + +
101B VAL 3.7 3.8 - - - +
103B LYS* 1.3 93.0 - - + +
105B MET* 1.3 58.8 + - + +
107B ASN* 3.6 2.3 - - - +
108B LYS* 2.8 41.3 + - + +
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Residues in contact with MET 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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122A ARG* 3.8 27.4 - - - +
154A VAL* 5.4 3.6 - - + -
90B LEU* 4.4 5.4 - - - -
101B VAL* 3.0 32.4 + - - +
102B TRP* 3.3 22.0 - - + +
104B ILE* 1.3 78.8 - - + +
106B LEU* 1.3 62.1 + - - +
108B LYS* 3.4 2.4 + - - -
109B GLU* 3.3 18.5 + - - +
229B LEU* 3.4 38.7 - - + +
234B TRP* 3.9 25.5 - - + -
237B VAL* 3.9 31.6 - - + -
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Residues in contact with LEU 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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102B TRP* 2.8 66.4 + - + +
103B LYS* 3.3 8.5 + - - +
105B MET* 1.3 72.1 - - - +
107B ASN* 1.3 65.4 + - - +
109B GLU* 3.3 25.3 + - - +
110B LYS* 3.6 21.5 + - - +
234B TRP* 4.1 9.4 - - + -
304B TYR* 3.9 22.4 - - + +
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Residues in contact with ASN 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 LYS* 2.8 38.8 + - - +
104B ILE* 4.1 2.7 - - - +
106B LEU* 1.3 77.6 - - - +
108B LYS* 1.3 64.8 + - - +
109B GLU 3.2 0.4 - - - -
110B LYS* 3.2 34.3 + - - +
111B THR* 3.4 12.4 + - - +
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Residues in contact with LYS 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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57A GLU* 3.1 26.0 + - - +
121A HIS 5.7 2.4 + - - -
122A ARG* 4.4 11.5 - - - +
104B ILE* 2.8 21.4 + - + +
105B MET* 3.8 8.3 - - - +
107B ASN* 1.3 73.9 - - - +
109B GLU* 1.3 61.7 + - - +
110B LYS 2.9 10.3 + - - -
111B THR* 2.9 27.4 + - + +
112B TYR* 3.2 19.2 - - + -
227B SER* 2.4 40.9 + - - +
228B PRO 4.4 0.4 - - - -
229B LEU* 3.6 34.8 - - + +
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Residues in contact with GLU 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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105B MET 3.3 8.0 + - - +
106B LEU* 3.3 20.8 - - - +
107B ASN 3.2 0.2 - - - -
108B LYS* 1.3 83.3 - - + +
110B LYS* 1.3 60.9 + - + +
111B THR 3.6 0.4 - - - -
112B TYR* 3.7 19.3 - - - +
114B ARG* 4.4 9.5 + - - +
229B LEU* 5.3 4.9 - - + +
234B TRP* 3.9 19.1 + - + +
280B PRO* 3.5 23.4 - - + +
281B TYR* 3.5 5.8 + - + +
282B GLY* 3.1 31.2 + - - -
304B TYR* 3.8 15.1 + - - -
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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