Contacts of the helix formed by residues 97 - 105 (chain B) in PDB entry 2WAL
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 ASP 97 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149A ASN* 3.5 23.0 + - + +
95B VAL* 3.6 8.6 - - + +
96B GLY* 1.3 77.0 - - - +
98B VAL* 1.3 59.1 + - - +
99B GLN* 3.2 19.9 + - - +
100B ARG* 2.9 56.3 + - + +
101B LEU* 3.1 25.1 + - - +
157B LEU* 4.4 3.7 - - + +
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Residues in contact with VAL 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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63B ALA* 4.2 5.4 - - + +
64B ALA* 3.5 17.9 - - - +
65B GLY* 3.5 30.5 - - - +
68B ASP* 4.4 4.7 - - - +
96B GLY 3.9 0.8 + - - -
97B ASP* 1.3 71.6 + - - +
99B GLN* 1.3 60.4 + - - +
101B LEU* 3.5 8.4 - - + +
102B ALA* 3.0 25.4 + - + +
117B LEU* 4.1 27.2 - - + +
118B HIS* 4.6 11.2 - - + -
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Residues in contact with GLN 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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97B ASP* 3.2 18.8 + - - +
98B VAL* 1.3 78.0 - - - +
100B ARG* 1.3 59.5 + - - +
102B ALA* 2.8 24.5 + - + +
103B ALA* 2.9 13.7 + - - +
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Residues in contact with ARG 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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97B ASP* 2.9 39.6 + - + +
99B GLN* 1.3 77.9 - - + +
101B LEU* 1.3 62.1 + - - +
103B ALA* 3.4 20.8 + - + +
104B ILE* 3.7 12.3 + - + +
156B THR* 5.4 2.8 - - - +
157B LEU* 3.4 35.5 + - + -
158B PRO 3.0 16.8 + - - -
159B GLU* 3.0 43.0 + - + +
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Residues in contact with LEU 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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30B LEU* 4.1 23.6 - - + -
61B VAL* 4.7 9.4 - - + -
63B ALA* 3.4 31.2 - - + -
95B VAL* 4.5 4.7 - - + -
97B ASP 3.1 15.4 + - - +
98B VAL 3.5 9.6 - - - +
99B GLN 3.1 0.2 - - - -
100B ARG* 1.3 75.4 - - - +
102B ALA* 1.3 58.8 + - - +
104B ILE* 3.0 19.1 + - + +
105B VAL* 3.2 26.5 + - + +
117B LEU* 4.3 21.1 - - + +
120B ILE* 4.1 12.8 - - + -
157B LEU* 4.0 17.4 - - + +
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Residues in contact with ALA 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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98B VAL* 3.0 15.1 + - + +
99B GLN* 2.8 16.4 + - - +
101B LEU* 1.3 74.7 - - - +
103B ALA* 1.3 61.7 + - - +
105B VAL 2.7 28.1 + - - +
106B GLY* 4.7 1.7 - - - -
108B GLY* 5.9 8.5 - - - -
117B LEU* 4.5 10.3 - - + +
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Residues in contact with ALA 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 GLN 2.9 9.0 + - - +
100B ARG* 3.4 18.6 - - + +
101B LEU 3.2 0.6 - - - -
102B ALA* 1.3 76.0 - - - +
104B ILE* 1.3 60.8 + - + +
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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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27B HIS* 4.3 31.6 - - + +
30B LEU* 4.0 33.0 - - + -
31B LEU* 3.4 34.1 - - + +
34B GLN* 3.6 8.1 - - - +
100B ARG* 3.8 17.0 - - + +
101B LEU* 3.0 7.9 + - - +
103B ALA* 1.3 81.4 - - + +
105B VAL* 1.3 59.2 + - + +
157B LEU* 3.9 32.5 - - + -
158B PRO* 5.9 0.4 - - + -
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Residues in contact with VAL 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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30B LEU* 5.3 4.7 - - + -
34B GLN* 3.1 36.1 - - - +
39B LEU* 4.0 18.2 - - + -
101B LEU* 3.5 29.4 - - + +
102B ALA* 2.7 30.0 + - - +
104B ILE* 1.3 83.1 - - + +
106B GLY* 1.3 72.0 + - - +
107B ALA* 5.9 0.4 - - + -
117B LEU* 3.6 12.5 - - + +
120B ILE* 4.3 10.5 - - + -
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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