Contacts of the helix formed by residues 98 - 103 (chain B) in PDB entry 2WLV
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 ARG 98 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B TRP* 3.9 3.6 - - - +
80B ASP* 3.2 52.2 + - - +
83B HIS* 2.3 34.9 + - - +
84B PRO* 4.3 0.6 - - - +
85B ILE* 3.9 40.2 - - - +
95B ARG* 5.4 4.0 - - + -
96B GLU* 4.3 11.7 - - - +
97B PRO* 1.3 81.0 + - - +
99B GLY* 1.3 68.3 + - - +
100B SER* 3.2 12.1 - - - +
101B ASP* 2.9 29.2 + - - +
102B ILE* 3.0 12.0 + - - +
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Residues in contact with GLY 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B ALA* 3.7 30.1 - - - -
79B TRP* 3.6 9.3 - - - -
80B ASP* 2.8 21.5 + - - -
98B ARG* 1.3 71.5 - - - +
100B SER* 1.3 56.4 + - - +
102B ILE* 3.2 5.7 + - - +
103B ALA* 3.0 24.1 + - - +
132B TRP* 3.7 12.2 - - - -
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Residues in contact with SER 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B ALA* 4.3 4.0 - - - +
80B ASP* 5.0 1.8 + - - -
98B ARG* 4.3 9.4 - - - +
99B GLY* 1.3 76.9 - - - +
101B ASP* 1.3 59.6 + - - +
102B ILE 3.4 0.2 - - - -
103B ALA* 3.6 5.2 + - - +
104B GLY 3.2 2.3 + - - -
105B THR* 2.9 44.8 + - - -
106B THR* 2.7 31.4 + - - +
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Residues in contact with ASP 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B PRO* 4.5 0.2 - - - +
95B ARG* 2.9 43.7 + - - -
97B PRO* 3.7 3.9 - - + +
98B ARG* 2.9 37.8 + - - +
100B SER* 1.3 74.0 - - - +
102B ILE* 1.3 66.5 + - - +
104B GLY* 3.1 4.3 + - - -
106B THR* 2.7 25.8 + - - +
107B SER* 2.7 23.1 + - - -
112B GLN* 4.5 4.7 - - - +
115B TRP* 3.6 24.2 - - + -
125B VAL* 5.3 0.2 - - - +
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Residues in contact with ILE 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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48B PRO* 3.1 26.2 - - - +
79B TRP* 3.3 60.6 - - + +
97B PRO* 4.2 5.2 - - + +
98B ARG 3.0 6.6 + - - +
99B GLY 3.2 7.4 + - - +
101B ASP* 1.3 76.4 - - - +
103B ALA* 1.3 56.1 + - - +
104B GLY 3.1 0.2 - - - -
125B VAL* 3.7 41.7 - - + +
128B ILE* 3.8 17.7 - - + -
129B TYR* 3.4 10.8 - - + +
132B TRP* 3.5 20.9 - - + -
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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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48B PRO* 4.2 0.2 - - - -
52B ASN* 2.9 18.5 + - - +
72B ILE* 3.8 29.6 - - + -
76B ALA* 5.5 0.9 - - + -
99B GLY 3.0 15.6 + - - +
100B SER* 3.6 7.4 + - - +
101B ASP 3.2 0.2 - - - -
102B ILE* 1.3 76.8 - - - +
104B GLY* 1.4 60.4 + - - +
105B THR* 3.3 14.9 + - + +
129B TYR* 3.4 25.1 + - + +
132B TRP* 4.3 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