Contacts of the helix formed by residues 59 - 68 (chain A) in PDB entry 1WE7
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 SER 59 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A ASP* 4.5 9.7 + - - -
57A GLN* 3.0 4.2 - - - -
58A VAL* 1.3 77.4 - - - +
60A VAL* 1.3 59.5 + - - +
62A LYS* 2.8 24.6 + - - +
63A VAL* 2.9 16.5 + - - +
87A ASP* 3.6 32.2 - - - +
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Residues in contact with VAL 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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52A LEU* 5.2 12.2 - - + +
56A ASP* 3.1 40.6 - - + +
57A GLN 2.8 22.6 + - - +
59A SER* 1.3 77.8 - - - +
61A ILE* 1.3 68.1 + - + +
63A VAL* 3.2 16.2 - - + +
64A LYS* 3.0 36.5 - - - +
91A LEU* 4.5 6.5 - - + -
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Residues in contact with ILE 61 (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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28A ILE* 4.5 27.1 - - + -
30A VAL* 4.5 3.6 - - + -
50A PHE* 5.7 3.5 - - + -
52A LEU* 6.2 3.4 - - + -
58A VAL* 2.7 40.8 + - + +
60A VAL* 1.3 80.6 - - + +
62A LYS* 1.3 60.4 + - - +
64A LYS* 3.7 4.8 + - - +
65A ILE* 3.2 31.9 + - + +
78A LEU* 3.7 17.7 - - + -
85A ILE* 4.9 5.6 - - + -
91A LEU* 3.4 31.2 - - + -
96A MET* 5.4 1.8 - - + -
102A ILE* 5.2 9.4 - - + -
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Residues in contact with LYS 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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58A VAL* 4.0 7.9 - - - +
59A SER* 2.8 8.7 + - - +
61A ILE* 1.3 75.8 - - - +
63A VAL* 1.3 66.2 + - - +
64A LYS 3.2 0.2 + - - -
65A ILE* 3.2 2.7 + - - -
66A HIS* 3.0 22.2 + - - +
73A ALA* 3.8 24.5 - - + +
74A GLY* 3.7 14.3 + - - +
76A GLN* 3.3 48.6 + - - +
77A LYS* 5.1 1.8 - - - +
78A LEU* 3.8 28.9 - - + +
85A ILE 5.0 0.4 + - - -
86A LYS* 4.8 13.0 - - - +
87A ASP* 3.3 38.5 + - + +
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Residues in contact with VAL 63 (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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59A SER* 2.9 12.9 + - - +
60A VAL* 3.2 26.0 - - + +
62A LYS* 1.3 75.8 - - - +
64A LYS* 1.3 71.0 + - + +
66A HIS* 3.4 7.1 + - - +
67A GLU* 2.9 42.9 + - + +
73A ALA* 4.0 11.6 - - + +
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Residues in contact with LYS 64 (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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50A PHE* 4.3 36.2 - - + -
52A LEU* 3.9 33.6 - - + +
60A VAL* 3.0 31.4 + - - +
61A ILE* 3.8 6.7 - - - +
62A LYS 3.2 0.2 - - - -
63A VAL* 1.3 85.9 - - + +
65A ILE* 1.3 66.7 + - - +
67A GLU* 2.8 20.3 + - + +
68A ALA* 3.1 13.2 + - - +
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Residues in contact with ILE 65 (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 VAL* 3.8 39.3 - - + -
32A VAL* 5.9 1.3 - - + -
48A LEU* 4.3 22.4 - - + -
50A PHE* 4.9 4.9 - - + -
61A ILE* 3.2 20.4 - - + +
62A LYS 3.2 5.5 + - - +
64A LYS* 1.3 76.3 - - - +
66A HIS* 1.3 51.4 + - - +
68A ALA* 3.3 1.8 + - - +
69A THR* 2.7 54.2 + - + +
71A MET* 4.7 6.7 - - + -
76A GLN* 3.3 30.5 - - - +
78A LEU* 3.9 16.8 - - + -
104A LEU* 5.3 3.8 - - + -
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Residues in contact with HIS 66 (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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62A LYS 3.0 16.2 + - - +
63A VAL* 3.7 9.0 + - - +
65A ILE* 1.3 75.1 - - - +
67A GLU* 1.3 71.8 + - - +
68A ALA 4.0 0.2 - - - -
69A THR 2.5 19.7 - - - +
70A GLY* 4.0 7.0 + - - -
71A MET 2.9 32.7 + - - +
72A PRO* 3.5 12.7 - - + +
73A ALA* 3.8 19.7 + - + +
76A GLN* 4.5 0.4 - - - +
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Residues in contact with GLU 67 (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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63A VAL* 2.9 29.1 + - + +
64A LYS* 2.8 18.5 + - + +
66A HIS* 1.3 84.2 + - - +
68A ALA* 1.3 58.5 + - + +
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Residues in contact with ALA 68 (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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42A LYS* 4.5 6.2 - - - +
48A LEU* 4.7 15.5 - - + -
50A PHE* 5.5 6.3 - - + -
64A LYS 3.1 9.1 + - - +
65A ILE 3.9 4.5 - - - +
67A GLU* 1.3 81.8 - - + +
69A THR* 1.3 67.7 + - + +
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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