Contacts of the helix formed by residues 68 - 77 (chain A) in PDB entry 1WL4
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 ASN 68 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A GLY 3.2 1.0 + - - -
67A GLN* 1.3 76.2 - - + +
69A PRO* 1.3 75.8 - - - +
70A VAL* 3.6 15.6 + - - +
71A ARG* 2.9 30.8 + - + +
72A GLN 3.3 5.9 + - - -
85A ALA 2.9 24.7 + - - -
86A TRP* 4.0 9.1 - - - +
87A SER* 4.3 7.1 + - - -
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Residues in contact with PRO 69 (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* 4.5 4.9 - - + -
31A GLN* 3.6 7.6 - - - +
59A HIS* 3.8 17.7 - - + +
62A ALA* 4.8 7.2 - - + +
65A CYS* 3.6 31.9 - - + +
66A GLY 3.4 9.4 - - - +
67A GLN 3.2 0.2 - - - -
68A ASN* 1.3 88.9 - - - +
70A VAL* 1.3 57.1 + - + +
72A GLN* 3.2 18.1 + - - +
73A ALA* 2.8 27.5 + - - +
119A MET* 3.7 17.7 - - + +
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Residues in contact with VAL 70 (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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55A VAL* 3.9 21.0 - - + +
57A PHE* 3.5 34.5 - - + +
59A HIS* 4.9 3.1 - - + -
68A ASN* 3.0 8.3 + - - +
69A PRO* 1.3 78.2 - - + +
71A ARG* 1.3 58.7 + - - +
73A ALA* 3.2 5.6 + - + +
74A SER* 2.8 27.2 + - - -
85A ALA* 4.2 0.9 - - + -
86A TRP 3.4 25.6 - - - +
87A SER* 3.6 26.0 - - - -
119A MET* 3.9 16.4 - - + -
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Residues in contact with ARG 71 (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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67A GLN 5.5 0.4 - - - +
68A ASN* 2.9 32.0 + - + +
70A VAL* 1.3 76.3 - - - +
72A GLN* 1.3 66.1 + - + +
74A SER* 3.3 1.2 + - - -
75A VAL* 3.0 34.7 + - + +
80A PRO 4.3 1.0 + - - -
81A TYR* 2.9 60.5 + - - +
83A VAL 2.9 23.6 + - - -
84A PRO* 4.5 3.2 - - - +
85A ALA* 3.7 21.9 - - + +
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Residues in contact with GLN 72 (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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31A GLN* 2.5 34.1 + - + +
35A SER* 3.9 0.5 + - - -
65A CYS 3.0 23.8 + - - -
66A GLY* 3.7 6.9 - - - -
67A GLN 2.9 28.0 + - - +
68A ASN 3.3 1.1 + - - +
69A PRO* 3.2 13.4 + - - +
71A ARG* 1.3 79.3 - - + +
73A ALA* 1.3 56.5 + - - +
75A VAL* 4.0 3.7 - - - +
76A GLY* 2.9 27.5 + - - -
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Residues in contact with ALA 73 (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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31A GLN* 3.4 21.3 - - - +
34A GLY* 4.0 10.3 - - - -
35A SER* 2.7 36.3 + - - +
38A ILE* 4.0 9.0 - - + -
57A PHE* 5.9 0.4 - - + -
69A PRO 2.8 14.2 + - - +
70A VAL* 3.2 11.9 + - + +
72A GLN* 1.3 76.8 - - - +
74A SER* 1.3 62.4 + - - +
77A ALA* 3.0 10.4 + - - +
119A MET* 4.5 5.2 - - - -
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Residues in contact with SER 74 (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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38A ILE* 4.0 9.8 - - - +
55A VAL* 3.5 17.9 - - - +
70A VAL 2.8 17.0 + - - -
71A ARG* 3.7 5.2 - - - -
73A ALA* 1.3 77.6 - - - +
75A VAL* 1.3 65.3 + - - +
77A ALA* 3.1 12.5 + - - +
79A ILE* 3.1 45.3 + - - +
80A PRO 5.2 0.2 + - - -
83A VAL 4.7 3.9 + - - -
85A ALA* 3.9 18.1 - - - +
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Residues in contact with VAL 75 (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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71A ARG* 3.0 34.7 + - + +
72A GLN* 4.1 3.8 - - - +
74A SER* 1.3 76.0 - - - +
76A GLY* 1.3 59.8 + - - +
78A GLY* 3.0 19.6 + - - -
79A ILE 3.4 16.7 - - - +
80A PRO 4.8 1.8 - - - +
81A TYR* 3.8 44.2 - - + +
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Residues in contact with GLY 76 (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 SER* 3.4 22.2 + - - -
39A LYS* 5.6 1.7 - - - +
72A GLN 2.9 14.3 + - - -
75A VAL* 1.3 77.0 - - - +
77A ALA* 1.3 57.7 + - - +
78A GLY 3.3 1.5 + - - -
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Residues in contact with ALA 77 (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 SER* 3.6 19.3 - - - +
38A ILE* 3.5 31.0 - - + -
39A LYS* 3.7 30.7 - - - +
42A LEU* 5.5 1.6 - - + +
49A PRO* 5.2 3.1 - - - +
73A ALA 3.0 11.1 + - - +
74A SER 3.1 11.1 + - - +
76A GLY* 1.3 77.0 - - - +
78A GLY* 1.3 57.3 + - - +
79A ILE* 4.6 3.2 - - + +
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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