Contacts of the helix formed by residues 51 - 67 (chain A) in PDB entry 1OVM
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 51 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A VAL* 3.8 8.7 - - - -
49A CYS* 3.4 2.6 - - - +
50A ALA* 1.3 77.3 - - - +
52A GLU* 1.3 70.0 + - - +
53A LEU* 3.1 9.7 + - - +
54A ASN* 2.7 51.3 + - - +
55A ALA* 3.1 18.4 + - - +
81A SER* 6.2 0.9 - - - -
440A LEU 5.3 2.2 + - - -
443A GLN* 3.7 15.8 + - - +
444A GLU* 4.1 0.8 + - - -
51B ASN* 5.8 1.8 - - - +
53B LEU* 6.1 4.3 - - + +
440B LEU* 3.3 37.2 + - + +
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Residues in contact with GLU 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A VAL* 3.1 32.9 - - + +
51A ASN* 1.3 75.0 - - - +
53A LEU* 1.3 65.5 + - - +
55A ALA* 3.5 9.2 - - + +
56A SER* 2.9 23.2 + - - -
71A LEU* 4.5 0.3 - - - +
73A THR* 3.9 19.9 - - + -
74A THR* 5.2 0.3 - - - +
78A GLY* 3.1 34.5 - - - +
81A SER* 3.2 16.6 - - - -
82A ALA* 3.7 6.9 - - + +
440B LEU* 3.7 11.1 - - - +
600B TPP 3.2 32.9 + - - +
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Residues in contact with LEU 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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51A ASN* 3.1 11.4 + - - +
52A GLU* 1.3 76.6 - - - +
54A ASN* 1.3 71.0 + - - +
56A SER* 2.7 29.2 + - - +
57A TYR* 3.0 54.2 + - + +
81A SER* 3.6 24.7 + - - +
84A ASN* 4.2 10.1 - - + -
85A GLY 4.0 11.7 - - - +
440A LEU* 5.2 5.4 - - + +
441A THR* 4.5 4.3 - - + -
51B ASN* 6.3 2.7 - - + -
53B LEU* 6.5 1.1 - - + -
81B SER* 5.0 11.7 - - - +
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Residues in contact with ASN 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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51A ASN* 2.7 28.8 + - - +
53A LEU* 1.3 79.7 - - - +
55A ALA* 1.3 56.2 + - - +
57A TYR* 3.0 4.5 + - - +
58A ALA* 2.8 30.4 + - - +
415A ALA* 3.7 8.0 - - + +
440A LEU 4.5 1.0 + - - -
441A THR* 3.3 41.0 - - - +
443A GLN* 3.5 24.4 - - - +
444A GLU* 2.8 39.7 - - + +
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Residues in contact with ALA 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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24A PHE* 4.0 3.7 - - + +
25A GLY* 3.9 14.4 - - - +
49A CYS* 3.7 27.1 - - + +
51A ASN 3.1 14.3 + - - +
52A GLU* 3.5 10.5 - - - +
53A LEU 3.2 0.2 - - - -
54A ASN* 1.3 76.7 - - - +
56A SER* 1.3 57.3 + - - +
58A ALA* 3.2 3.6 + - - +
59A ALA* 2.9 29.5 + - - +
71A LEU* 3.5 21.5 - - + -
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Residues in contact with SER 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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52A GLU 2.9 13.9 + - - -
53A LEU* 2.7 23.0 + - - +
55A ALA* 1.3 77.7 - - - +
57A TYR* 1.3 62.6 + - - +
59A ALA* 3.4 5.1 + - - +
60A ASP* 3.0 22.3 + - - +
71A LEU* 3.8 25.0 - - - +
82A ALA* 3.8 8.7 + - - -
85A GLY* 3.3 31.3 - - - -
86A ILE* 4.5 3.6 - - - -
89A SER* 4.9 2.3 + - - -
96A VAL* 5.2 1.8 - - - +
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Residues in contact with TYR 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 LEU* 3.0 51.1 + - + +
54A ASN* 3.0 2.9 + - - +
56A SER* 1.3 78.0 + - - +
58A ALA* 1.3 56.3 - - - +
60A ASP* 3.1 7.7 + - + +
61A GLY 2.9 24.1 + - - -
84A ASN* 3.0 14.3 + - - -
85A GLY* 4.1 16.8 - - - -
404A GLN* 5.4 2.0 - - - -
407A TRP* 5.9 0.4 - + - -
409A SER* 2.8 27.0 + - - -
410A ILE 4.4 3.9 + - - -
411A GLY* 4.1 0.4 - - - -
412A TYR* 3.4 50.0 - + + +
415A ALA* 3.4 25.8 - - + -
416A ALA* 3.5 9.8 - - - +
441A THR* 3.7 15.9 - - + -
600A TPP 5.2 0.9 - - - +
81B SER* 4.7 0.7 + - - -
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Residues in contact with ALA 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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24A PHE* 4.0 22.0 - - + -
49A CYS* 4.7 0.4 - - - -
54A ASN 2.8 12.2 + - - +
55A ALA* 3.4 11.4 - - - +
57A TYR* 1.3 74.0 - - - +
59A ALA* 1.3 59.7 + - - +
61A GLY 3.2 1.2 + - - -
62A TYR* 2.8 26.1 + - - +
415A ALA* 3.5 20.6 + - + +
416A ALA* 4.2 0.2 - - - +
418A PHE* 4.0 10.1 - - + -
419A GLY* 3.3 20.3 - - - +
444A GLU* 5.7 0.2 - - + -
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Residues in contact with ALA 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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24A PHE* 3.9 20.5 - - + -
55A ALA 2.9 16.9 + - - +
56A SER* 3.7 7.4 - - - +
57A TYR 3.3 0.2 - - - -
58A ALA* 1.3 75.4 - - - +
60A ASP* 1.3 57.4 + - - +
62A TYR 3.2 0.2 + - - -
63A ALA* 2.8 25.8 + - - +
69A ALA* 3.0 20.0 - - + +
70A ALA 4.2 7.9 - - - +
71A LEU* 4.5 4.7 - - + -
96A VAL* 3.9 23.8 - - + -
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Residues in contact with ASP 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 SER 3.0 14.3 + - - +
57A TYR* 3.1 10.5 + - + +
59A ALA* 1.3 77.3 - - - +
61A GLY* 1.3 62.7 + - - +
63A ALA 3.1 2.1 + - - -
64A ARG* 2.9 39.9 + - - +
85A GLY 4.6 2.0 - - - +
88A GLY 4.3 1.6 - - - -
89A SER* 2.7 37.5 + - - +
94A VAL* 3.6 12.7 - - - +
96A VAL* 3.9 10.3 - - - +
404A GLN* 4.7 0.9 + - - -
412A TYR* 2.6 35.7 + - + -
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Residues in contact with GLY 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 TYR 2.9 11.6 + - - -
58A ALA 3.2 2.9 + - - -
60A ASP* 1.3 76.6 + - - +
62A TYR* 1.3 63.7 + - - +
64A ARG* 3.1 14.7 + - - +
65A CYS* 3.4 18.0 + - - -
402A ILE* 4.3 6.6 - - - +
412A TYR* 4.0 10.5 + - - -
416A ALA* 3.8 18.6 - - - -
420A ALA 4.2 6.5 - - - -
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Residues in contact with TYR 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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20A ALA* 4.3 11.7 - - + -
21A ASP 2.9 19.5 + - - -
22A HIS* 2.8 46.3 + + + -
24A PHE* 3.6 22.9 - + + -
58A ALA 2.8 16.6 + - - +
59A ALA 3.5 4.9 - - - +
61A GLY* 1.3 76.5 - - - +
63A ALA* 1.3 56.9 + - - +
65A CYS* 2.9 6.2 + - - +
66A LYS* 2.9 50.6 + - + +
68A PHE 3.4 22.0 - - - -
69A ALA* 3.9 7.0 - - + -
419A GLY 3.6 23.2 - - - +
422A THR* 4.1 0.7 - - + -
423A ALA* 3.6 21.3 - - + -
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Residues in contact with ALA 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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59A ALA 2.8 14.5 + - - +
60A ASP 3.1 0.2 + - - -
62A TYR* 1.3 71.9 - - - +
64A ARG* 1.3 58.0 + - - +
65A CYS 3.0 5.8 - - - -
67A GLY* 2.7 29.5 + - - -
68A PHE* 3.7 21.8 - - - +
69A ALA* 3.7 13.5 - - + +
94A VAL* 3.5 26.7 - - + -
95A PRO* 3.9 10.2 - - + +
96A VAL* 4.3 0.9 - - + -
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Residues in contact with ARG 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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60A ASP* 2.9 41.0 + - - +
61A GLY* 3.1 8.9 + - - +
63A ALA* 1.3 76.9 - - - +
65A CYS* 1.3 59.7 + - - +
67A GLY 4.7 0.2 - - - -
92A GLU* 3.0 32.7 + - - +
94A VAL* 3.8 13.3 - - + +
222A ARG* 3.1 38.0 - - - +
245A MET 5.7 2.2 + - - -
400A ASN* 3.3 15.5 + - - +
401A PHE 5.6 0.6 + - - -
402A ILE* 3.7 36.1 - - + +
403A VAL 3.0 25.3 + - - +
404A GLN* 4.3 7.9 - - - +
412A TYR* 3.2 9.6 + - - -
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Residues in contact with CYS 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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61A GLY 3.5 14.6 - - - -
62A TYR 2.9 7.2 + - - +
64A ARG* 1.3 82.5 - - - +
66A LYS* 1.3 61.7 + - - +
67A GLY 3.5 0.4 - - - -
378A ILE* 4.4 6.3 - - - -
400A ASN* 3.7 18.8 - - - +
402A ILE* 4.3 5.4 - - - -
420A ALA* 3.9 25.6 - - - -
423A ALA* 3.9 15.3 - - + -
424A CYS* 3.9 19.6 - - - -
427A ARG* 6.3 0.2 - - - -
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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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18A CYS 5.1 0.7 - - - +
19A GLY* 3.8 24.8 - - - +
21A ASP* 2.5 32.8 + - - +
22A HIS* 4.8 4.0 + - - -
62A TYR* 2.9 45.0 + - + +
65A CYS* 1.3 80.3 - - - +
67A GLY* 1.3 60.1 + - - +
68A PHE* 3.2 6.9 + - - +
423A ALA* 3.7 30.8 + - + +
424A CYS* 5.6 1.1 - - - -
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Residues in contact with GLY 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 CYS 5.2 0.2 - - - -
63A ALA 2.7 24.6 + - - -
64A ARG 4.7 0.2 - - - -
65A CYS 3.5 1.8 - - - -
66A LYS* 1.3 71.3 - - - +
68A PHE* 1.3 61.7 + - - +
95A PRO* 2.9 23.4 - - - +
160A ARG* 3.4 18.0 + - - -
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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