Contacts of the helix formed by residues 52 - 62 (chain A) in PDB entry 1W2I
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 GLU 52 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A ALA* 2.8 52.0 + - - +
4A VAL* 3.7 29.1 - - + +
50A GLY 3.4 0.2 + - - -
51A ASP* 1.3 71.3 - - - +
53A GLU* 1.3 61.5 + - + +
55A VAL* 3.4 0.7 + - - +
56A GLU* 2.9 49.1 + - - +
64B GLN* 5.3 6.7 + - - +
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Residues in contact with GLU 53 (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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51A ASP* 3.3 3.4 - - + +
52A GLU* 1.3 81.7 - - + +
54A ARG* 1.3 69.2 + - + +
56A GLU* 3.9 9.5 - - - +
57A ALA* 3.0 26.2 + - - +
29B LYS* 5.1 8.7 + - - -
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Residues in contact with ARG 54 (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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29A LYS 4.9 2.0 + - - -
30A LEU* 2.9 61.5 + - + +
31A GLY* 4.8 4.4 - - - +
32A VAL* 3.7 17.5 - - + +
51A ASP* 3.1 24.0 + - + +
53A GLU* 1.3 84.7 + - + +
55A VAL* 1.3 67.4 + - - +
57A ALA* 3.3 7.1 + - - +
58A LEU* 3.1 17.8 + - - +
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Residues in contact with VAL 55 (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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4A VAL* 3.9 16.6 - - + -
6A ALA* 4.0 16.8 - - + -
32A VAL* 4.2 10.5 - - + -
48A LEU* 4.0 14.8 - - + +
49A GLU 3.8 8.5 - - - +
50A GLY* 3.4 34.8 - - - +
51A ASP 2.9 16.3 + - - +
52A GLU 3.9 3.4 - - - +
54A ARG* 1.3 75.5 - - - +
56A GLU* 1.3 57.7 + - - +
58A LEU* 3.1 4.8 + - - +
59A ILE* 2.9 44.4 + - + +
78A TRP* 4.3 2.2 - - + -
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Residues in contact with GLU 56 (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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4A VAL* 6.2 0.4 - - + -
52A GLU* 2.9 34.1 + - + +
53A GLU* 3.9 8.5 - - - +
55A VAL* 1.3 75.7 - - + +
57A ALA* 1.3 62.7 + - - +
59A ILE* 4.3 4.3 - - - -
60A GLY* 3.0 19.9 + - - -
78A TRP* 4.8 11.8 - - + -
26B GLU* 5.5 1.6 - - - +
56B GLU 3.9 1.7 - - - +
57B ALA* 4.5 6.1 - - - +
60B GLY* 3.3 31.4 - - - +
61B TRP* 3.7 30.6 - - - +
64B GLN* 3.9 22.7 + - - +
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Residues in contact with ALA 57 (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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30A LEU* 3.9 24.0 - - + -
53A GLU* 3.0 16.0 + - + +
54A ARG* 3.4 9.9 - - - +
55A VAL 3.2 0.4 - - - -
56A GLU* 1.3 76.7 - - - +
58A LEU* 1.3 58.1 + - - +
60A GLY* 3.4 1.4 + - - -
61A TRP* 3.0 26.9 + - - +
56B GLU* 4.4 5.6 - - - +
57B ALA* 4.7 16.1 - - + +
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Residues in contact with LEU 58 (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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23A MET* 4.2 12.6 - - + +
26A GLU* 3.7 31.0 - - + -
27A ALA* 3.7 30.3 - - + +
30A LEU* 3.7 13.2 - - + -
32A VAL* 3.8 12.6 - - + -
48A LEU* 3.7 29.6 - - + -
54A ARG 3.1 9.8 + - - +
55A VAL 3.7 6.1 - - - +
57A ALA* 1.3 75.6 - - - +
59A ILE* 1.3 65.5 + - - +
61A TRP* 3.2 18.3 + - + +
62A ALA* 3.0 22.8 + - + +
87A PHE* 4.4 5.2 - - + -
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Residues in contact with ILE 59 (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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6A ALA* 3.8 15.0 - - + -
8A LEU* 4.1 11.2 - - + -
48A LEU* 3.8 16.4 - - + -
55A VAL* 2.9 20.0 + - + +
56A GLU* 3.3 11.4 + - - +
58A LEU* 1.3 76.1 - - - +
60A GLY* 1.3 60.4 + - - +
62A ALA* 3.1 14.9 + - - +
63A HIS* 2.8 25.6 + - + -
76A VAL* 4.3 11.4 - - + -
78A TRP* 3.7 33.4 - - + -
60B GLY* 3.9 10.5 - - - +
63B HIS* 3.7 29.8 - - + -
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Residues in contact with GLY 60 (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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56A GLU 3.0 11.1 + - - -
57A ALA 3.8 0.7 - - - -
59A ILE* 1.3 74.0 - - - +
61A TRP* 1.3 65.1 + - - +
63A HIS* 3.0 24.3 + - - +
64A GLN* 3.9 1.6 + - - +
56B GLU* 3.2 40.4 - - - +
59B ILE* 4.1 4.6 - - - +
60B GLY* 3.9 7.1 - - - -
78B TRP* 5.1 0.5 - - - -
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Residues in contact with TRP 61 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A PHE* 3.8 20.2 - + - -
22A SER* 3.4 32.5 - - - -
23A MET* 3.5 33.7 - - + -
26A GLU* 3.5 34.2 + - + +
30A LEU* 5.8 1.6 - - + -
57A ALA 3.0 15.5 + - - +
58A LEU* 3.2 24.7 + - + +
60A GLY* 1.3 75.0 - - - +
62A ALA* 1.3 77.3 + - + +
64A GLN* 2.9 9.8 + - + +
65A GLY* 2.8 52.5 + - - -
66A PRO* 3.9 1.5 - - + +
56B GLU* 3.6 27.4 - - - +
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Residues in contact with ALA 62 (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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8A LEU* 4.3 11.0 - - + -
10A ILE* 4.0 27.1 - - + +
19A PHE* 3.5 8.4 - - + -
23A MET* 4.3 7.2 - - + -
48A LEU* 6.0 0.2 - - + -
58A LEU* 3.0 14.3 + - + +
59A ILE 3.4 11.7 - - - +
60A GLY 3.1 0.4 - - - -
61A TRP* 1.3 91.4 - - + +
63A HIS* 1.3 60.4 + - - +
64A GLN 3.3 0.4 - - - -
65A GLY 4.0 1.1 - - - -
71A VAL* 3.5 19.9 - - - +
74A VAL* 4.3 1.5 - - + +
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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