Contacts of the helix formed by residues 61 - 73 (chain A) in PDB entry 1WH5
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 61 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A THR* 5.8 2.2 - - + -
24A PHE* 5.9 0.2 - - + -
55A CYS* 4.4 0.9 - - + -
59A GLY 3.7 4.0 - - - +
60A VAL* 1.4 97.3 - - + +
62A ARG* 1.3 54.5 + - - +
63A GLN* 4.5 4.9 - - + +
64A VAL* 2.7 35.2 + - + +
65A LEU* 2.7 31.5 + - - +
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Residues in contact with ARG 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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43A ILE* 4.9 17.7 - - + +
48A ASP* 5.0 3.8 + - - -
51A ILE* 3.9 25.8 - - + -
52A GLN* 4.7 22.4 - - + +
55A CYS* 4.1 10.1 - - - -
60A VAL 3.7 2.4 + - - -
61A PRO* 1.3 69.3 - - - +
63A GLN* 1.3 68.3 + - - +
65A LEU* 2.7 21.5 + - - +
66A LYS* 2.8 13.4 + - + +
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Residues in contact with GLN 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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15A GLY* 5.7 3.4 - - - -
16A ILE* 2.7 37.9 - - + +
17A ARG* 3.0 18.6 + - - +
18A LYS* 3.9 17.4 - - - +
19A ARG* 4.0 8.8 - - - +
61A PRO* 3.2 6.2 - - + +
62A ARG* 1.3 80.7 - - - +
64A VAL* 1.3 59.5 + - + +
66A LYS* 3.6 13.4 + - - +
67A VAL* 3.0 42.6 + - + +
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Residues in contact with VAL 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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19A ARG* 4.7 16.4 - - + -
20A HIS 5.2 1.6 - - - +
22A THR* 4.0 18.2 - - + -
24A PHE* 3.5 27.8 - - + -
60A VAL* 3.0 25.6 - - + -
61A PRO* 2.7 33.3 + - + +
63A GLN* 1.3 78.5 - - + +
65A LEU* 1.3 49.0 + - - -
66A LYS 2.8 4.8 + - - -
67A VAL* 3.6 6.3 - - + -
68A TRP* 2.6 43.9 + - + +
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Residues in contact with LEU 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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32A MET* 3.2 40.2 - - + -
35A LEU* 3.6 27.6 - - + -
39A ILE* 4.5 0.7 - - + -
43A ILE* 4.4 2.7 - - + -
51A ILE* 4.0 22.4 - - + -
54A PHE* 3.5 21.5 - - + -
55A CYS* 4.9 3.4 - - - -
60A VAL* 4.5 3.6 - - + -
61A PRO 2.7 15.3 + - - +
62A ARG* 2.7 13.6 + - - +
64A VAL* 1.3 75.3 - - - +
66A LYS* 1.3 55.1 + - - +
68A TRP* 4.1 4.5 - - + -
69A LEU* 2.9 35.2 + - + +
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Residues in contact with LYS 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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43A ILE* 3.3 30.3 - - + -
62A ARG* 2.8 13.9 + - + +
63A GLN* 3.6 14.1 - - - +
64A VAL 2.8 0.6 - - - -
65A LEU* 1.3 76.4 - - - +
67A VAL* 1.3 80.0 + - + +
68A TRP 3.1 0.7 - - - -
69A LEU* 3.0 23.0 + - + +
70A HIS* 3.4 3.9 + - - +
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Residues in contact with VAL 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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18A LYS* 6.6 0.4 - - + -
19A ARG* 4.2 19.7 - - + +
63A GLN* 3.0 32.5 - - + +
64A VAL* 3.3 12.1 - - + +
66A LYS* 1.3 89.2 - - + +
68A TRP* 1.3 59.8 + - - +
70A HIS* 2.5 18.9 + - + +
71A ASN* 2.4 50.9 + - - +
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Residues in contact with TRP 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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24A PHE* 3.4 38.9 - + + +
29A LYS* 3.5 20.0 - - + +
32A MET* 3.1 60.7 - - + +
33A LEU* 3.4 24.7 - - + -
41A TRP* 4.1 6.3 - + - -
64A VAL* 2.6 30.9 + - + +
65A LEU 4.1 2.5 - - - +
67A VAL* 1.3 73.0 - - - +
69A LEU* 1.3 96.8 + - + +
71A ASN* 2.5 15.6 + - + +
72A ASN* 2.5 77.9 + - + +
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Residues in contact with LEU 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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32A MET* 4.6 0.9 - - + +
36A ALA* 3.0 39.7 - - + +
39A ILE* 4.7 1.1 - - + -
41A TRP* 3.6 39.0 - - + +
42A ARG 4.2 2.7 - - - +
43A ILE* 4.0 15.3 - - + -
65A LEU* 2.9 36.6 - - + +
66A LYS 3.0 10.1 + - - +
68A TRP* 1.3 93.7 - - + +
70A HIS* 1.3 54.2 + - - +
72A ASN* 4.3 0.2 - - - -
73A LYS* 2.5 43.7 + - + +
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Residues in contact with HIS 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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66A LYS 3.4 1.9 + - - +
67A VAL* 2.5 24.1 + - - +
69A LEU* 1.3 71.0 - - - +
71A ASN* 1.3 58.4 + - - +
72A ASN 2.9 4.5 - - - -
73A LYS* 2.9 41.5 + - + +
74A HIS* 4.6 21.0 + + + +
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Residues in contact with ASN 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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19A ARG* 3.7 39.1 + - - +
24A PHE* 5.7 4.7 - - + -
67A VAL* 2.4 47.6 + - - +
68A TRP* 2.5 16.2 + - + +
70A HIS* 1.3 75.9 - - - +
72A ASN* 1.3 61.4 + - - +
73A LYS 4.3 0.2 - - - -
75A SER 4.8 3.5 - - - +
76A GLY* 5.6 0.2 - - - -
77A PRO* 5.2 4.0 - - - +
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Residues in contact with ASN 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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29A LYS* 4.7 6.6 - - - +
33A LEU* 4.6 6.4 - - - +
41A TRP* 3.6 17.7 - - + -
68A TRP* 2.5 84.1 + - + +
69A LEU 3.5 2.9 - - - +
70A HIS 2.9 0.6 - - - -
71A ASN* 1.3 77.9 + - - +
73A LYS* 1.3 70.1 + - - +
75A SER 3.2 18.2 - - - +
76A GLY* 3.9 6.9 - - - -
77A PRO* 4.4 15.8 - - + +
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Residues in contact with LYS 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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40A GLY 5.5 0.2 - - - -
41A TRP* 3.4 53.5 + - + -
69A LEU* 2.5 36.1 + - + +
70A HIS* 2.9 34.6 + - + +
71A ASN 4.3 0.2 - - - -
72A ASN* 1.3 85.9 - - - +
74A HIS* 1.3 77.1 + - + +
75A SER 3.6 0.7 - - - +
78A SER* 6.2 0.9 - - - -
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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