Contacts of the helix formed by residues 46 - 62 (chain A) in PDB entry 4OWW
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 ASP 46 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A LEU* 3.5 22.7 - - + +
39A SER* 5.9 3.0 + - - +
44A ALA 3.5 3.2 + - - +
45A LYS* 1.3 73.1 - - - +
47A GLU* 1.3 65.9 + - - +
48A LEU* 3.0 27.4 + - - +
49A GLU* 3.0 22.8 + - + +
50A GLU* 3.0 27.4 + - - +
133A LYS* 2.5 35.8 + - - +
136A LYS* 3.3 20.6 + - - +
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Residues in contact with GLU 47 (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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45A LYS* 3.6 24.1 + - - +
46A ASP* 1.3 74.0 + - - +
48A LEU* 1.3 63.2 + - - +
50A GLU* 3.4 3.4 + - - +
51A ARG* 3.1 22.9 + - + +
54A ARG* 3.6 25.0 + - - -
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Residues in contact with LEU 48 (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 LEU* 5.1 2.7 - - + -
37A LEU* 5.5 3.1 - - + -
46A ASP* 3.0 10.8 + - - +
47A GLU* 1.3 75.7 - - - +
49A GLU* 1.3 72.3 + - + +
51A ARG* 3.2 6.7 + - - +
52A LEU* 3.0 45.1 + - + +
125A LYS* 4.3 15.9 - - + +
128A GLN* 3.3 46.7 - - + +
129A ILE* 4.1 18.2 - - + -
133A LYS* 4.1 21.7 - - + +
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Residues in contact with GLU 49 (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 ARG* 3.3 17.7 - - - +
36A LEU* 3.1 26.1 + - + +
37A LEU* 2.9 44.4 + - + +
39A SER* 4.8 6.9 + - - -
46A ASP* 3.0 31.9 + - + +
48A LEU* 1.3 81.6 - - - +
50A GLU* 1.3 63.5 + - - +
52A LEU* 3.4 2.1 + - - +
53A GLU* 3.0 47.3 + - - +
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Residues in contact with GLU 50 (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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45A LYS* 4.6 27.0 - - + +
46A ASP 3.0 18.8 + - - +
47A GLU* 3.7 8.7 - - - +
48A LEU 3.2 0.2 - - - -
49A GLU* 1.3 85.1 - - - +
51A ARG* 1.3 61.4 + - - +
53A GLU* 3.1 25.0 + - - +
54A ARG* 3.2 48.4 + - + +
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Residues in contact with ARG 51 (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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47A GLU* 3.1 19.7 + - + +
48A LEU* 3.2 6.3 + - - +
50A GLU* 1.3 74.3 - - - +
52A LEU* 1.3 68.7 + - + +
54A ARG* 3.1 25.6 + - - +
55A CYS* 3.0 33.5 + - - -
84A PRO 5.8 0.4 + - - -
87A GLU* 2.2 44.8 + - - +
88A GLU* 5.4 4.8 - - - +
91A LEU* 3.6 14.5 - - + +
125A LYS* 3.5 25.4 - - - +
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Residues in contact with LEU 52 (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 LEU* 3.6 26.7 - - + -
48A LEU* 3.0 35.8 + - + +
49A GLU 3.8 4.5 - - - +
51A ARG* 1.3 80.2 - - + +
53A GLU* 1.3 56.9 + - - +
55A CYS* 3.4 3.8 + - - +
56A MET* 3.0 28.1 + - - +
91A LEU* 3.6 35.9 - - + +
94A PHE* 4.1 7.9 - - + -
95A THR* 3.2 27.9 + - + +
125A LYS* 3.9 15.3 - - + -
129A ILE* 4.1 15.7 - - + -
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Residues in contact with GLU 53 (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 ARG* 3.5 40.6 + - - +
36A LEU* 4.3 3.1 + - + -
49A GLU* 3.0 30.7 + - + +
50A GLU* 3.1 35.1 - - - +
51A ARG 3.1 0.4 - - - -
52A LEU* 1.3 74.5 - - - +
54A ARG* 1.3 61.4 + - + +
56A MET* 3.5 24.4 + - + +
57A SER* 3.0 25.5 + - - -
95A THR* 5.5 2.0 - - + -
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Residues in contact with ARG 54 (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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45A LYS* 5.6 2.8 - - - +
47A GLU* 3.6 20.4 + - - -
50A GLU* 3.2 33.8 + - + +
51A ARG* 3.1 35.0 + - - +
53A GLU* 1.3 74.9 - - - +
55A CYS* 1.3 60.8 + - - +
57A SER* 2.9 10.1 + - - -
58A ILE* 2.9 36.3 + - + +
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Residues in contact with CYS 55 (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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51A ARG* 3.0 32.2 + - - -
52A LEU* 3.7 7.6 - - - +
53A GLU 3.4 0.2 - - - -
54A ARG* 1.3 77.1 - - - +
56A MET* 1.3 62.4 + - - +
58A ILE* 3.4 10.5 + - - +
59A VAL* 3.1 27.5 + - - +
88A GLU* 3.3 35.0 - - - +
91A LEU* 3.9 26.9 - - + -
92A GLY* 3.6 12.1 - - - +
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Residues in contact with MET 56 (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 ARG 5.4 4.9 - - - +
52A LEU 3.0 15.8 + - - +
53A GLU* 3.6 22.4 - - + +
55A CYS* 1.3 76.7 - - - +
57A SER* 1.3 62.3 + - - +
59A VAL* 3.4 3.3 + - - +
60A THR* 3.1 26.9 + - + +
92A GLY* 3.7 11.8 - - - +
95A THR* 3.6 25.1 - - + +
96A LEU* 3.6 31.4 - - + -
99A THR* 3.3 29.2 - - + +
100A GLU* 5.1 3.6 - - - +
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Residues in contact with SER 57 (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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53A GLU 3.0 13.4 + - - -
54A ARG* 2.9 14.0 + - - -
56A MET* 1.3 74.9 - - - +
58A ILE* 1.3 65.6 + - - +
60A THR* 3.2 8.4 + - - -
61A SER* 3.0 25.9 + - - -
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Residues in contact with ILE 58 (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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54A ARG* 2.9 25.3 + - + +
55A CYS* 3.5 10.3 - - - +
57A SER* 1.3 77.6 - - - +
59A VAL* 1.3 63.2 + - + +
61A SER* 3.3 16.3 + - - -
62A MET* 3.3 23.1 + - - +
78A TYR* 4.0 31.4 - - + +
88A GLU* 4.0 21.8 - - + +
89A ILE* 4.7 5.2 - - + -
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Residues in contact with VAL 59 (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 CYS 3.1 15.1 + - - +
56A MET 3.7 8.1 - - - +
57A SER 3.3 0.2 - - - -
58A ILE* 1.3 76.0 - - - +
60A THR* 1.3 55.3 + - - +
62A MET* 3.3 4.9 + - - +
63A THR* 2.7 39.7 + - + +
75A LEU* 4.5 12.6 - - + -
89A ILE* 3.7 33.0 - - + +
92A GLY* 3.6 19.5 - - - -
93A LEU* 4.0 13.9 - - + -
96A LEU* 3.6 26.7 - - + -
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Residues in contact with THR 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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56A MET* 3.1 19.6 + - + +
57A SER* 3.2 12.3 + - - -
59A VAL* 1.3 70.7 - - - +
61A SER* 1.3 59.3 + - - +
62A MET 3.1 2.0 - - - -
63A THR* 3.2 9.4 - - - +
64A ALA* 2.8 42.1 + - - +
96A LEU* 4.3 26.5 - - + -
103A GLN* 5.3 6.1 - - - +
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Residues in contact with SER 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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57A SER 3.0 19.0 + - - -
58A ILE* 3.5 9.4 - - - -
59A VAL 3.3 0.4 - - - -
60A THR* 1.3 78.1 + - - +
62A MET* 1.3 62.1 + - - +
63A THR 3.7 0.3 + - - -
64A ALA* 4.5 7.0 + - - +
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Residues in contact with MET 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 ILE* 3.3 23.3 + - - +
59A VAL 3.3 6.8 + - - +
60A THR 3.1 0.4 - - - -
61A SER* 1.3 80.3 - - - +
63A THR* 1.3 64.6 + - + +
64A ALA 5.4 0.7 - - - -
66A VAL* 4.5 4.3 - - - +
70A GLU 4.6 0.2 - - - +
71A ALA* 3.9 5.5 - - - +
74A ALA* 3.5 38.0 - - + +
75A LEU* 3.6 26.5 - - + -
78A TYR* 3.5 50.5 - - + -
89A ILE* 3.8 3.1 - - + -
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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