Contacts of the helix formed by residues 61 - 76 (chain A) in PDB entry 1OMW
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 GLN 61 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A GLU* 4.1 14.7 + - - -
57A LYS* 2.7 29.9 + - - +
58A ILE* 3.2 9.3 + - - +
60A SER* 1.3 80.1 - - - +
62A LYS* 1.3 66.8 + - - +
64A GLY 4.2 5.2 - - - +
65A TYR* 3.0 24.7 + - - +
174A PHE* 3.5 23.0 - - - -
178A LYS* 2.8 31.6 + - - -
514A SER* 5.0 4.5 - - - +
518A GLN* 3.0 24.2 + - - +
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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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60A SER 4.2 0.8 + - - -
61A GLN* 1.3 72.3 - - - +
63A LEU* 1.3 58.4 + - - +
65A TYR* 3.7 8.5 - - + +
66A LEU* 3.2 35.3 + - + +
515A GLU 5.7 1.3 - - - +
518A GLN* 3.3 23.4 + - + +
519A GLN* 3.1 39.6 + - - +
522A ALA* 4.0 24.2 - - + +
523A GLU* 6.0 0.2 - - - +
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Residues in contact with LEU 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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62A LYS* 1.3 74.2 - - - +
64A GLY* 1.3 64.8 + - - +
65A TYR 3.2 1.1 - - - -
66A LEU* 3.6 5.4 + - + +
67A LEU* 3.1 36.7 + - + +
174A PHE* 4.4 5.8 - - + -
177A TRP* 4.6 11.9 - - + -
517A TRP* 3.9 20.2 - - + -
518A GLN* 2.9 62.5 + - + +
521A VAL* 4.4 7.9 - - + -
522A ALA* 4.2 12.3 - - + +
526A PHE* 3.8 35.8 - - + -
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Residues in contact with GLY 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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58A ILE* 3.6 35.2 - - - +
61A GLN* 3.3 4.4 + - - +
63A LEU* 1.3 76.1 - - - +
65A TYR* 1.3 53.4 + - - +
67A LEU* 3.4 2.0 + - - +
68A PHE* 2.7 38.2 + - - +
165A PHE* 4.7 0.7 - - - -
174A PHE* 3.8 19.3 - - - -
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Residues in contact with TYR 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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58A ILE 4.0 1.2 + - - -
59A PHE* 3.6 53.6 - + - +
61A GLN 3.0 17.3 + - - +
62A LYS* 3.7 9.4 - - + +
63A LEU 3.2 0.2 - - - -
64A GLY* 1.3 77.4 - - - +
66A LEU* 1.3 67.6 + - + +
68A PHE* 3.0 5.2 + - - +
69A ARG* 2.7 60.5 + - + +
83A VAL* 4.4 4.4 - - + +
86A TYR* 3.7 17.4 - + - -
87A GLU* 2.9 37.2 + - - +
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Residues in contact with LEU 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* 3.2 28.7 + - + +
63A LEU* 3.8 6.3 - - + +
65A TYR* 1.3 89.4 - - + +
67A LEU* 1.3 57.1 + - - +
69A ARG* 3.5 24.2 - - - +
70A ASP* 3.0 36.0 + - - +
522A ALA* 4.3 21.8 - - + +
526A PHE* 3.7 35.0 - - + -
527A ASP* 5.7 1.3 - - - +
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Residues in contact with LEU 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 LEU* 3.1 24.3 + - + +
64A GLY* 4.0 2.7 - - - +
66A LEU* 1.3 73.1 - - - +
68A PHE* 1.3 67.7 + - - +
70A ASP* 3.2 8.0 + - - +
71A PHE* 3.1 23.6 + - - +
165A PHE* 3.7 8.3 - - + -
170A LYS* 3.9 28.2 - - + +
173A ARG* 3.9 29.4 - - + +
174A PHE* 3.7 34.1 - - + +
177A TRP* 4.7 3.8 - - + -
526A PHE* 4.3 20.6 - - + -
530A ASN* 4.7 7.0 - - - +
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Residues in contact with PHE 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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55A PHE* 3.7 22.7 - + - -
58A ILE* 5.3 3.8 - - + -
59A PHE* 3.5 37.5 - + + -
64A GLY 2.7 24.7 + - - +
65A TYR* 3.5 5.6 - + - +
67A LEU* 1.3 74.9 - - - +
69A ARG* 1.3 61.6 + - + +
71A PHE* 3.3 3.6 + - - +
72A CYS* 3.0 53.8 + - - -
83A VAL* 5.0 3.1 - - + -
157A LEU* 4.1 22.9 - - + -
161A VAL* 4.3 4.9 - - + -
162A PHE* 4.5 14.1 - + - -
165A PHE* 3.5 44.5 - + + -
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Residues in contact with ARG 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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65A TYR* 2.7 40.0 + - + +
66A LEU* 3.5 25.6 + - - +
68A PHE* 1.3 73.4 - - + +
70A ASP* 1.3 74.5 + - - +
72A CYS* 4.1 7.2 - - - +
73A LEU* 2.8 49.6 + - + +
83A VAL* 3.9 18.2 - - + -
87A GLU* 2.8 40.6 + - - -
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Residues in contact with ASP 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 LEU* 3.0 22.1 + - - +
67A LEU* 3.2 9.8 + - + +
69A ARG* 1.3 92.8 + - - +
71A PHE* 1.3 57.4 + - - +
73A LEU* 4.7 3.6 - - - +
74A LYS* 2.9 58.0 + - + +
75A HIS* 4.1 2.4 - - - -
170A LYS* 4.5 18.7 + - + +
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Residues in contact with PHE 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 LEU 3.1 9.8 + - - +
68A PHE 3.4 7.4 - - - +
70A ASP* 1.3 79.6 - - - +
72A CYS* 1.3 71.7 + - - +
75A HIS* 3.2 39.7 + + + -
76A LEU* 3.4 38.1 + - + -
161A VAL 3.9 8.7 - - - -
164A LYS* 3.4 26.0 - - + -
165A PHE* 3.5 40.4 - + + -
168A SER* 3.8 19.3 - - - -
170A LYS* 3.7 12.0 - - + +
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Residues in contact with CYS 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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68A PHE* 3.0 63.3 + - - +
69A ARG 3.2 1.8 + - - +
71A PHE* 1.3 85.5 - - - +
73A LEU* 1.3 62.0 + - - +
76A LEU* 2.9 27.5 + - - +
79A ALA* 3.9 21.9 - - + +
80A LYS* 3.7 8.9 + - - +
83A VAL* 3.5 25.8 - - + -
157A LEU* 4.9 0.4 - - - -
161A VAL* 4.2 3.4 - - - -
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Residues in contact with LEU 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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69A ARG* 2.8 50.0 + - - +
70A ASP* 4.3 2.7 - - - +
72A CYS* 1.3 78.6 - - - +
74A LYS* 1.3 66.1 + - + +
76A LEU 4.8 1.0 - - - +
80A LYS* 3.5 38.6 - - + +
83A VAL* 4.3 13.5 - - + -
84A GLU* 3.7 38.6 - - + +
87A GLU* 4.4 7.4 - - - +
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Residues in contact with LYS 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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70A ASP* 2.9 41.9 + - + +
73A LEU* 1.3 80.0 - - + +
75A HIS* 1.3 76.7 + - + +
76A LEU 3.9 0.4 - - - -
77A GLU* 5.2 5.3 - - - +
170A LYS* 5.9 2.9 - - - +
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Residues in contact with HIS 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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70A ASP 4.1 4.9 - - - -
71A PHE* 3.2 31.7 + + + +
74A LYS* 1.3 97.5 + - + +
76A LEU* 1.3 69.9 + - - +
77A GLU* 4.3 2.7 - - - -
170A LYS* 3.7 32.7 + - + -
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Residues in contact with LEU 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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71A PHE* 3.4 37.4 + - + +
72A CYS 2.9 18.5 + - - +
73A LEU 4.8 0.7 - - - +
74A LYS 3.9 0.6 - - - -
75A HIS* 1.3 84.8 - - - +
77A GLU* 1.3 69.4 + - - +
78A GLU* 4.0 22.7 - - + +
79A ALA* 3.5 12.5 + - + -
80A LYS* 3.8 5.7 + - - +
161A VAL* 3.9 31.4 - - + -
164A LYS* 3.9 33.4 - - + +
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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