Contacts of the helix formed by residues 73 - 87 (chain A) in PDB entry 1WMH
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 73 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A PHE* 3.7 15.8 - - - -
71A VAL* 3.7 1.4 - - - +
72A SER* 1.3 82.1 - - - +
74A GLN* 1.3 65.0 + - - +
75A LEU* 3.5 8.6 + - - +
76A GLU* 2.8 34.0 + - - +
77A LEU* 3.0 23.9 + - - +
49B VAL* 5.9 1.9 - - - +
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Residues in contact with GLN 74 (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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35A SER 5.4 1.2 - - - +
36A ILE 4.3 4.7 - - - +
37A SER* 3.5 19.1 - - - +
38A PHE* 2.8 41.0 - - + +
39A GLU 4.8 0.2 - - - +
73A SER* 1.3 73.8 - - - +
75A LEU* 1.3 62.7 + - - +
77A LEU* 3.8 3.0 - - - +
78A GLU* 3.0 59.6 + - - +
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Residues in contact with LEU 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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73A SER* 3.2 9.5 + - - +
74A GLN* 1.3 81.0 - - - +
76A GLU* 1.3 62.4 + - + +
78A GLU* 3.4 15.8 + - + +
79A GLU* 3.3 18.7 + - - +
29B PHE* 3.8 28.8 - - + +
30B ALA 4.0 19.0 + - - +
31B LEU* 6.0 0.7 - - + -
45B LEU* 4.1 16.8 - - + -
49B VAL* 3.9 22.4 - - + -
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Residues in contact with GLU 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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61A TRP* 4.6 4.9 + - - +
70A THR 3.2 13.2 - - - +
71A VAL* 4.0 16.0 - - + +
72A SER* 2.8 23.4 + - - -
73A SER* 2.8 24.6 + - - +
75A LEU* 1.3 76.7 - - + +
77A LEU* 1.3 66.1 + - - +
79A GLU* 3.3 3.6 + - - +
80A ALA* 3.1 21.7 + - - +
27B ARG* 2.8 41.9 + - - +
28B ARG 3.7 21.9 - - - +
29B PHE* 4.9 2.7 - - + -
49B VAL* 3.5 19.8 - - + +
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Residues in contact with LEU 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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36A ILE* 3.9 5.2 - - + +
37A SER 3.8 6.7 - - - +
38A PHE* 3.6 32.8 - - + +
41A LEU* 3.6 32.8 - - + -
71A VAL* 3.7 19.0 - - + +
73A SER 3.0 17.9 + - - +
74A GLN* 3.8 7.0 - - - +
76A GLU* 1.3 75.8 - - - +
78A GLU* 1.3 65.0 + - + +
80A ALA* 3.1 11.3 + - + +
81A PHE* 3.0 52.9 + - + -
92A LEU* 5.3 2.0 - - + -
94A ILE* 5.8 2.7 - - + -
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Residues in contact with GLU 78 (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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34A PRO 6.1 0.4 - - - +
74A GLN* 3.0 51.8 + - - +
75A LEU* 3.7 16.1 - - + +
76A GLU 3.2 0.2 - - - -
77A LEU* 1.3 78.4 - - + +
79A GLU* 1.3 56.4 + - - +
81A PHE* 3.4 11.2 + - + +
82A ARG* 2.8 28.3 + - - +
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Residues in contact with GLU 79 (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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75A LEU 3.3 5.7 + - - +
76A GLU 3.3 8.2 + - - +
77A LEU 3.2 0.6 - - - -
78A GLU* 1.3 75.8 - - - +
80A ALA* 1.3 68.4 + - - +
82A ARG* 2.7 46.0 + - - -
83A LEU* 3.0 39.2 + - + +
17B GLU* 3.5 15.6 - - - +
28B ARG* 3.7 9.7 + - + +
29B PHE* 3.6 34.1 - - - +
30B ALA* 3.2 19.2 - - - +
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Residues in contact with ALA 80 (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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61A TRP* 3.7 46.7 - - + +
71A VAL* 5.7 0.7 - - + -
76A GLU 3.1 10.8 + - - +
77A LEU* 3.4 15.7 - - + +
79A GLU* 1.3 74.4 - - - +
81A PHE* 1.3 60.1 + - - +
83A LEU* 4.0 1.4 - - - +
84A TYR* 3.1 27.9 + - - +
92A LEU* 4.3 20.1 - - + +
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Residues in contact with PHE 81 (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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17A VAL* 3.8 39.7 - - + -
19A VAL* 5.1 1.1 - - + -
32A PHE* 4.5 8.1 - - + -
33A GLU 4.4 0.7 - - - -
34A PRO* 3.4 29.6 - - + +
36A ILE* 3.7 33.4 - - + -
41A LEU* 4.0 9.0 - - + -
77A LEU* 3.0 44.6 + - + -
78A GLU* 3.7 10.5 - - + +
80A ALA* 1.3 75.9 - - - +
82A ARG* 1.3 64.1 + - - +
84A TYR* 3.3 5.2 + - - +
85A GLU* 3.2 29.2 + - + +
92A LEU* 3.9 17.5 - - + -
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Residues in contact with ARG 82 (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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78A GLU 2.8 18.4 + - - +
79A GLU* 2.7 43.8 + - - +
81A PHE* 1.3 78.6 - - - +
83A LEU* 1.3 65.9 + - - +
85A GLU* 3.4 5.3 + - - +
86A LEU* 2.9 45.1 + - + +
15B ILE* 4.3 30.6 - - - +
17B GLU* 3.3 32.1 + - - +
30B ALA* 3.9 10.4 - - - +
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Residues in contact with LEU 83 (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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61A TRP* 3.7 23.8 - - + -
79A GLU* 3.0 35.6 + - + +
80A ALA 4.1 2.2 - - - +
82A ARG* 1.3 96.8 - - - +
84A TYR* 1.3 61.2 + - - +
86A LEU* 4.2 13.9 - - + -
87A ASN* 2.8 51.1 + - - +
89A ASP* 4.7 1.1 - - - +
17B GLU* 3.8 15.5 - - - +
28B ARG* 3.6 33.0 - - - +
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Residues in contact with TYR 84 (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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16A GLN 3.7 8.2 + - - -
17A VAL* 3.7 26.5 - - + -
18A ARG* 3.0 25.9 + - - +
61A TRP* 6.0 1.3 - - - -
80A ALA 3.1 19.3 + - - +
81A PHE* 3.4 7.4 - - + +
83A LEU* 1.3 76.9 - - - +
85A GLU* 1.3 88.3 + - + +
88A LYS* 3.2 2.4 + - - -
89A ASP* 3.0 69.2 + - + +
90A SER 3.5 11.8 + - - -
91A GLU* 3.7 21.1 - - - -
92A LEU* 3.7 22.9 - - + -
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Residues in contact with GLU 85 (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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16A GLN 4.4 4.3 + - - +
17A VAL* 4.1 8.7 - - + +
34A PRO* 4.7 12.7 - - + +
81A PHE* 3.2 15.1 + - + +
82A ARG* 3.8 7.4 - - - +
84A TYR* 1.3 102.8 - - - +
86A LEU* 1.3 65.6 + - - +
88A LYS* 3.0 20.3 + - - +
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Residues in contact with LEU 86 (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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82A ARG* 2.9 41.0 + - + +
83A LEU* 3.9 18.8 - - + +
85A GLU* 1.3 78.1 - - - +
87A ASN* 1.3 67.8 + - - +
88A LYS* 3.4 13.9 + - - +
17B GLU* 4.7 5.8 - - - +
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Residues in contact with ASN 87 (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 GLU* 4.0 32.8 + - + +
83A LEU* 2.8 44.7 + - - +
86A LEU* 1.3 80.3 - - - +
88A LYS* 1.3 76.1 + - - +
89A ASP* 3.2 24.1 + - - +
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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