Contacts of the helix formed by residues 51 - 67 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A LEU* 6.3 2.9 - - + -
440A LEU* 3.4 35.0 + - + +
26B VAL* 3.8 8.7 - - - -
49B CYS* 3.4 2.8 - - - +
50B ALA* 1.3 76.1 - - - +
52B GLU* 1.3 69.1 + - - +
53B LEU* 3.1 11.0 + - - +
54B ASN* 2.7 46.5 + - - +
55B ALA* 3.1 18.0 + - - +
81B SER* 6.3 0.4 - - - -
440B LEU 5.3 2.0 + - - -
443B GLN* 3.5 25.3 + - - +
444B GLU* 4.1 0.6 + - - -
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Residues in contact with GLU 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A LEU* 4.0 4.7 - - - +
600A TPP 2.7 45.7 + - - +
26B VAL* 2.9 25.4 - - + +
51B ASN* 1.3 77.2 - - - +
53B LEU* 1.3 66.2 + - - +
55B ALA* 3.4 8.8 - - - +
56B SER* 2.9 24.6 + - - -
71B LEU* 4.5 0.5 - - - +
73B THR* 3.9 17.2 - - + -
74B THR* 5.1 0.5 - - - +
78B GLY* 3.3 34.5 - - - +
81B SER* 3.7 13.6 - - - -
82B ALA* 3.8 5.6 - - + +
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Residues in contact with LEU 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ASN* 6.1 4.5 - - + +
53A LEU* 6.5 1.3 - - + -
81A SER* 4.9 14.6 - - - +
51B ASN* 3.1 10.4 + - - +
52B GLU* 1.3 77.3 - - - +
54B ASN* 1.3 71.1 + - - +
56B SER* 2.6 28.8 + - - +
57B TYR* 3.0 52.8 + - + +
81B SER* 3.5 22.9 + - - +
84B ASN* 4.2 7.2 - - + -
85B GLY 4.0 12.8 - - - +
440B LEU* 5.1 5.6 - - + +
441B THR* 4.5 4.0 - - + -
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Residues in contact with ASN 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B ASN* 2.7 37.9 + - - +
53B LEU* 1.3 77.8 - - - +
55B ALA* 1.3 53.5 + - - +
57B TYR* 3.0 4.3 + - - +
58B ALA* 2.8 36.2 + - - +
415B ALA* 3.7 8.4 - - + +
440B LEU 4.5 0.8 + - - -
441B THR* 3.2 49.8 - - - +
443B GLN* 3.5 7.1 - - - +
444B GLU* 2.8 39.3 - - + +
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Residues in contact with ALA 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B PHE* 4.0 3.3 - - - +
25B GLY* 3.9 13.0 - - - +
49B CYS* 3.7 28.4 - - + +
51B ASN 3.1 13.9 + - - +
52B GLU* 3.4 12.8 - - - +
53B LEU 3.2 0.4 - - - -
54B ASN* 1.3 77.6 - - - +
56B SER* 1.3 56.2 + - - +
58B ALA* 3.2 3.8 + - - +
59B ALA* 2.8 29.1 + - - +
71B LEU* 3.5 20.2 - - + -
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Residues in contact with SER 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B GLU 2.9 12.3 + - - -
53B LEU* 2.6 25.9 + - - +
55B ALA* 1.3 75.8 - - - +
57B TYR* 1.3 63.4 + - - +
59B ALA* 3.3 5.8 + - - +
60B ASP* 3.0 22.0 + - - +
71B LEU* 3.8 26.4 - - - +
82B ALA* 3.9 8.7 + - - -
85B GLY* 3.3 30.7 - - - -
86B ILE* 4.5 3.4 - - - -
89B SER* 5.0 2.8 + - - -
96B VAL* 5.1 2.0 - - - +
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Residues in contact with TYR 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A SER* 4.8 0.5 + - - -
53B LEU* 3.0 51.5 + - + +
54B ASN* 3.4 6.7 - - - +
56B SER* 1.3 76.8 + - - +
58B ALA* 1.3 58.0 + - - +
60B ASP* 3.1 9.1 + - + +
61B GLY 2.9 24.4 + - - -
84B ASN* 3.0 13.7 + - - -
85B GLY* 4.2 16.2 - - - -
404B GLN* 5.3 2.2 - - - -
407B TRP* 5.9 0.2 - + - -
409B SER* 2.8 28.3 + - - -
410B ILE 4.2 4.4 + - - -
411B GLY* 4.0 0.4 - - - -
412B TYR* 3.4 48.7 - + + +
415B ALA* 3.4 21.5 - - + -
416B ALA* 3.6 8.6 - - - +
441B THR* 3.7 17.5 - - + -
600B TPP 5.1 0.9 - - - +
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Residues in contact with ALA 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B PHE* 3.9 25.6 - - + -
54B ASN 2.8 16.8 + - - +
55B ALA* 3.5 10.1 - - - +
57B TYR* 1.3 74.4 - - - +
59B ALA* 1.3 57.2 + - - +
61B GLY 3.2 0.7 + - - -
62B TYR* 2.8 26.9 + - - +
415B ALA* 3.3 19.7 + - + +
416B ALA* 4.2 0.4 - - - +
418B PHE* 4.1 10.5 - - + -
419B GLY* 3.3 16.3 - - - +
444B GLU* 5.7 0.2 - - + -
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Residues in contact with ALA 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B PHE* 3.8 20.1 - - + -
55B ALA 2.8 13.3 + - - +
56B SER* 3.6 10.8 - - - +
57B TYR 3.2 0.2 - - - -
58B ALA* 1.3 76.7 - - - +
60B ASP* 1.3 58.7 + - - +
62B TYR 3.3 0.2 + - - -
63B ALA* 2.8 26.0 + - - +
69B ALA* 3.0 19.8 - - + +
70B ALA 4.3 7.4 - - - +
71B LEU* 4.5 4.3 - - + -
96B VAL* 3.9 23.3 - - + -
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Residues in contact with ASP 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B SER 3.0 12.9 + - - +
57B TYR* 3.1 10.5 + - + +
59B ALA* 1.3 77.6 - - - +
61B GLY* 1.3 62.1 + - - +
63B ALA* 3.2 4.0 + - - +
64B ARG* 2.9 40.7 + - - +
85B GLY 4.6 1.8 - - - +
88B GLY 4.3 1.9 - - - -
89B SER* 2.7 39.1 + - - +
94B VAL* 3.6 10.4 - - - +
96B VAL* 3.9 10.7 - - - +
404B GLN* 4.8 0.7 + - - -
412B TYR* 2.7 35.6 + - + -
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Residues in contact with GLY 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B TYR 2.9 12.0 + - - -
58B ALA 3.7 2.9 - - - -
60B ASP* 1.3 76.2 + - - +
62B TYR* 1.3 62.8 + - - +
64B ARG* 3.1 16.9 + - - +
65B CYS* 3.4 15.6 + - - -
402B ILE* 4.3 7.4 - - - +
412B TYR* 4.0 4.9 + - - -
416B ALA* 3.8 24.0 - - - -
420B ALA 4.2 6.5 - - - -
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Residues in contact with TYR 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B ALA* 4.3 11.4 - - + -
21B ASP 2.9 18.9 + - - -
22B HIS* 2.8 47.0 + + + -
24B PHE* 3.6 21.5 - + + -
58B ALA 2.8 16.4 + - - +
59B ALA* 3.5 4.3 - - - +
61B GLY* 1.3 75.5 - - - +
63B ALA* 1.3 56.8 + - - +
65B CYS* 2.8 20.3 + - - +
66B LYS* 2.9 38.5 + - + +
68B PHE 3.4 22.9 - - - -
69B ALA* 3.8 7.4 - - + -
419B GLY 3.6 24.2 - - - +
422B THR* 4.0 1.8 - - + -
423B ALA* 3.6 21.5 - - + -
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Residues in contact with ALA 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B ALA 2.8 20.4 + - - +
62B TYR* 1.3 74.1 - - - +
64B ARG* 1.3 57.9 + - - +
65B CYS 3.0 0.4 - - - -
67B GLY* 2.7 30.0 + - - -
68B PHE 3.7 21.8 - - - +
69B ALA* 3.7 12.1 - - + -
94B VAL* 3.4 25.5 - - + +
95B PRO* 3.9 11.4 - - + +
96B VAL* 4.2 0.9 - - + -
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Residues in contact with ARG 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B ASP* 2.9 39.2 + - - +
61B GLY* 3.1 9.5 + - - +
63B ALA* 1.3 76.3 - - - +
65B CYS* 1.3 59.3 + - - +
67B GLY 4.7 0.2 - - - -
92B GLU* 2.9 31.7 + - - +
94B VAL* 3.9 11.9 - - + +
222B ARG* 3.3 40.4 - - - +
245B MET 5.8 1.8 + - - -
400B ASN* 3.4 14.9 + - - +
401B PHE 5.6 0.4 + - - -
402B ILE* 3.8 35.1 - - + +
403B VAL 2.8 27.3 + - - +
404B GLN* 4.1 8.9 - - - +
412B TYR* 3.2 11.1 + - - -
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Residues in contact with CYS 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B GLY 3.6 13.0 - - - -
62B TYR 2.8 7.9 + - - +
64B ARG* 1.3 82.3 - - - +
66B LYS* 1.3 62.9 + - - +
67B GLY 3.5 0.7 - - - -
378B ILE* 4.3 6.5 - - - -
400B ASN* 3.8 17.3 - - - -
402B ILE* 4.4 5.2 - - - -
420B ALA* 3.8 26.9 - - - -
423B ALA* 3.9 15.0 - - + -
424B CYS* 4.0 20.4 - - - -
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Residues in contact with LYS 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B CYS 5.2 0.7 - - - +
19B GLY* 3.7 25.5 - - - +
21B ASP* 2.4 36.9 + - - +
22B HIS* 5.0 3.4 + - - -
62B TYR* 2.9 39.8 + - + +
65B CYS* 1.3 79.6 - - + +
67B GLY* 1.3 59.3 + - - +
68B PHE* 3.2 6.9 + - - +
423B ALA* 3.7 31.1 + - + +
424B CYS* 5.8 0.7 - - - -
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Residues in contact with GLY 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B CYS 5.2 0.2 - - - -
63B ALA 2.7 24.3 + - - -
64B ARG 4.7 0.4 - - - -
65B CYS 3.5 1.4 - - - -
66B LYS* 1.3 71.7 - - - +
68B PHE* 1.3 61.7 + - - +
95B PRO* 3.0 22.5 - - - +
160B ARG* 3.3 18.6 + - - -
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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