Contacts of the helix formed by residues 98 - 107 (chain A) in PDB entry 3WAL
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 PRO 98 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A ASP 3.9 13.5 - - - +
61A HIS* 4.2 9.6 - - - +
62A VAL 3.5 7.0 - - - +
63A ASN* 3.6 10.3 - - - +
96A SER 3.5 5.8 - - - +
97A THR* 1.4 87.7 - - + +
99A ILE* 1.3 66.6 + - - +
100A ALA* 4.1 4.5 - - + +
101A ASP* 3.0 35.1 + - - +
102A ILE* 3.4 8.3 + - - +
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Residues in contact with ILE 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A ILE* 3.8 11.0 - - + -
37A VAL* 3.8 28.7 - - + -
58A VAL* 3.9 20.4 - - + -
59A PRO 3.5 24.7 - - - +
60A ASP* 3.5 10.3 + - - +
62A VAL* 2.8 18.8 + - + +
64A MET* 3.5 22.9 - - - -
67A LEU* 4.2 8.3 - - + -
97A THR 3.6 1.2 + - - -
98A PRO* 1.3 72.4 - - - +
100A ALA* 1.3 55.9 + - - +
102A ILE* 3.2 0.8 + - - -
103A TYR* 2.8 35.1 + - - +
113A LEU* 3.9 12.3 - - + -
115A MET* 4.0 14.8 - - + -
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Residues in contact with ALA 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A ILE* 4.3 13.5 - - + -
60A ASP* 3.0 40.3 + - + +
98A PRO* 3.1 4.7 - - + -
99A ILE* 1.3 75.5 - - - +
101A ASP* 1.3 63.4 + - - +
103A TYR* 3.4 3.6 - - - +
104A GLU* 3.3 30.7 + - - +
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Residues in contact with ASP 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A THR* 3.5 14.3 - - + +
98A PRO* 3.0 33.3 + - - +
100A ALA* 1.3 79.4 - - - +
102A ILE* 1.3 63.4 + - - +
103A TYR 3.2 1.1 - - - -
104A GLU* 3.5 7.1 + - - +
105A GLN* 3.2 37.3 + - - +
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Residues in contact with ILE 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A MET* 3.6 38.1 - - + -
87A VAL* 4.5 11.2 - - + -
92A MET* 4.9 7.0 - - + -
95A VAL* 4.5 7.9 - - + -
97A THR* 3.8 26.5 - - + +
98A PRO 3.4 1.5 + - - +
99A ILE 3.2 6.4 + - - +
101A ASP* 1.3 74.2 - - - +
103A TYR* 1.3 59.9 + - - +
105A GLN* 3.2 22.0 + - - +
106A GLU* 2.8 45.0 + - + +
113A LEU* 4.1 17.3 - - + -
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Residues in contact with TYR 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A VAL* 4.3 8.0 - - - +
28A ARG* 4.5 7.4 + - - +
35A ILE* 3.4 35.9 - - + -
36A PRO* 4.0 17.2 - - + +
99A ILE 2.8 17.5 + - - +
100A ALA 3.4 7.9 - - - +
101A ASP 3.2 0.2 - - - -
102A ILE* 1.3 76.9 - - - +
104A GLU* 1.3 74.5 + - + +
107A LYS* 2.8 64.3 + - + +
111A GLY* 2.7 37.5 + - - -
113A LEU* 4.1 17.5 - - + +
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Residues in contact with GLU 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A ALA 3.3 15.8 + - - +
101A ASP* 3.8 7.6 - - - +
102A ILE 3.3 0.2 - - - -
103A TYR* 1.3 92.2 - - + +
105A GLN* 1.3 61.8 + - + +
107A LYS* 3.4 34.9 + - - +
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Residues in contact with GLN 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A THR* 5.0 2.6 - - - +
101A ASP* 3.2 30.7 + - - +
102A ILE* 3.2 24.9 + - - +
104A GLU* 1.3 78.8 - - + +
106A GLU* 1.3 78.5 + - + +
107A LYS* 3.8 0.7 - - - -
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Residues in contact with GLU 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A VAL* 3.8 15.3 - - + -
88A ASN* 2.6 47.7 + - - +
90A HIS* 4.8 12.6 + - - -
102A ILE* 2.8 29.1 + - + +
105A GLN* 1.3 94.0 - - + +
107A LYS* 1.3 67.7 + - - +
108A ASP* 3.4 1.9 + - - -
113A LEU* 3.7 19.4 - - + +
114A TYR 5.4 1.0 + - - -
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Residues in contact with LYS 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A TYR* 2.8 57.2 + - + +
104A GLU* 3.4 41.3 + - - +
105A GLN 3.8 0.6 - - - -
106A GLU* 1.3 79.0 - - - +
108A ASP* 1.3 72.7 + - - +
109A GLU* 3.8 1.4 + - - +
111A GLY* 4.5 2.9 - - - +
112A PHE 3.6 6.1 - - - +
113A LEU* 4.1 6.0 - - - +
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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