Contacts of the helix formed by residues 51 - 67 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C VAL* 3.8 8.1 - - - -
49C CYS* 4.0 2.1 - - - +
50C ALA* 1.3 77.9 - - - +
52C GLU* 1.3 69.8 + - - +
53C LEU* 3.1 9.0 + - - +
54C ASN* 2.5 56.8 + - - +
55C ALA* 3.0 17.5 + - - +
81C SER* 6.3 0.4 - - - -
440C LEU 5.2 2.6 + - - -
443C GLN* 3.7 12.7 - - - +
444C GLU* 4.2 0.6 + - - -
51D ASN* 5.7 2.4 - - - +
53D LEU* 6.3 3.5 - - + +
440D LEU* 3.5 35.6 + - + +
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Residues in contact with GLU 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C VAL* 3.1 33.3 - - + +
51C ASN* 1.3 78.6 - - - +
53C LEU* 1.3 65.4 + - - +
55C ALA* 3.4 8.2 - - - +
56C SER* 2.9 23.9 + - - -
71C LEU* 4.5 0.3 - - - +
73C THR* 4.0 18.8 - - + -
74C THR* 5.3 0.2 - - - +
78C GLY* 3.1 34.6 - - - +
81C SER* 3.2 19.3 - - - -
82C ALA* 3.9 4.9 - - + +
440D LEU* 3.6 7.6 - - - +
600D TPP 3.1 30.8 + - - +
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Residues in contact with LEU 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C ASN* 3.1 11.2 + - - +
52C GLU* 1.3 76.4 - - - +
54C ASN* 1.3 72.6 + - - +
56C SER* 2.7 28.7 + - - +
57C TYR* 3.0 51.5 + - + +
81C SER* 3.5 25.5 + - - +
84C ASN* 4.1 8.7 - - + -
85C GLY 4.0 13.9 - - - +
440C LEU* 5.2 4.7 - - + +
441C THR* 4.5 4.3 - - + -
51D ASN* 6.2 3.1 - - + +
53D LEU* 6.4 3.4 - - + -
81D SER* 5.0 13.2 - - - +
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Residues in contact with ASN 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C CYS* 5.0 0.9 - - - -
51C ASN* 2.5 40.0 + - - +
53C LEU* 1.3 78.1 - - - +
55C ALA* 1.3 50.8 + - - +
57C TYR* 3.0 4.5 + - - +
58C ALA* 2.7 36.2 + - - +
415C ALA* 3.7 8.1 - - + +
440C LEU 4.5 0.4 + - - -
441C THR* 3.3 41.2 - - - +
443C GLN* 3.6 16.1 - - - +
444C GLU* 2.8 38.3 - - + +
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Residues in contact with ALA 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C PHE* 4.0 3.1 - - - +
25C GLY* 3.9 13.5 - - - +
49C CYS* 3.7 28.0 - - + +
51C ASN 3.0 14.2 + - - +
52C GLU* 3.4 13.7 - - - +
53C LEU 3.2 0.2 - - - -
54C ASN* 1.3 75.4 - - - +
56C SER* 1.3 57.3 + - - +
58C ALA* 3.1 4.1 + - - +
59C ALA* 2.8 29.6 + - - +
71C LEU* 3.5 19.7 - - + -
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Residues in contact with SER 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C GLU 2.9 13.7 + - - -
53C LEU* 2.7 21.5 + - - -
55C ALA* 1.3 77.5 - - - +
57C TYR* 1.3 62.9 + - - +
59C ALA* 3.4 5.3 + - - +
60C ASP* 3.0 21.8 + - - +
71C LEU* 3.8 25.3 - - - +
82C ALA* 3.8 10.5 + - - -
85C GLY* 3.2 31.6 + - - -
86C ILE* 4.5 3.4 - - - -
89C SER* 4.8 3.5 + - - -
96C VAL* 5.1 1.4 - - - +
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Residues in contact with TYR 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C LEU* 3.0 51.2 + - + +
54C ASN* 3.0 7.6 + - - +
56C SER* 1.3 76.7 + - - +
58C ALA* 1.3 63.7 + - - +
60C ASP* 3.1 8.7 + - + +
61C GLY 3.0 18.5 + - - -
84C ASN* 3.2 12.0 + - - -
85C GLY* 4.2 16.2 - - - -
404C GLN* 5.4 2.7 - - - -
407C TRP* 5.9 0.2 - + - -
409C SER* 2.8 29.4 + - - -
410C ILE 4.2 4.9 + - - -
411C GLY* 4.0 0.4 - - - -
412C TYR* 3.4 48.6 - + + +
415C ALA* 3.4 21.3 - - + -
416C ALA* 3.5 9.0 - - - +
441C THR* 3.7 17.7 - - + -
600C TPP 5.1 0.9 - - - +
81D SER* 4.8 0.9 + - - -
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Residues in contact with ALA 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C PHE* 3.9 24.5 - - + -
49C CYS* 4.9 0.4 - - - -
54C ASN 2.7 16.5 + - - +
55C ALA* 3.4 11.0 - - - +
57C TYR* 1.3 73.6 - - - +
59C ALA* 1.3 56.9 + - - +
61C GLY 3.1 0.9 + - - -
62C TYR* 2.8 27.3 + - - +
415C ALA* 3.4 21.3 + - + +
416C ALA* 4.2 0.2 - - - +
418C PHE* 4.0 10.3 - - + -
419C GLY* 3.3 15.8 - - - +
444C GLU* 5.7 0.2 - - + -
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Residues in contact with ALA 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C PHE* 3.9 20.1 - - + -
55C ALA 2.8 16.8 + - - +
56C SER* 3.6 8.3 - - - +
58C ALA* 1.3 75.3 - - - +
60C ASP* 1.3 58.2 + - - +
62C TYR 3.3 0.3 + - - -
63C ALA* 2.9 26.0 + - - +
69C ALA* 3.0 18.8 - - + +
70C ALA 4.2 7.4 - - - +
71C LEU* 4.5 4.7 - - + -
96C VAL* 4.0 23.3 - - + -
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Residues in contact with ASP 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C SER 3.0 13.1 + - - +
57C TYR* 3.1 10.1 + - + +
59C ALA* 1.3 77.6 - - - +
61C GLY* 1.3 62.1 + - - +
63C ALA* 3.2 4.3 + - - +
64C ARG* 2.9 39.1 + - - +
85C GLY 4.6 1.8 - - - +
88C GLY 4.3 2.4 - - - -
89C SER* 2.9 36.9 + - - +
94C VAL* 3.6 10.2 - - - +
96C VAL* 3.9 10.5 - - - +
404C GLN* 4.7 0.9 + - - -
412C TYR* 2.7 36.7 + - + -
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Residues in contact with GLY 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C TYR 3.0 11.8 + - - -
58C ALA 3.1 3.3 + - - -
60C ASP* 1.3 76.0 - - - +
62C TYR* 1.3 63.3 + - - +
64C ARG* 3.1 16.6 + - - +
65C CYS* 3.4 15.9 + - - -
402C ILE* 4.3 7.0 - - - +
412C TYR* 4.1 5.5 + - - -
416C ALA* 3.8 24.2 - - - -
420C ALA* 4.2 6.5 - - - -
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Residues in contact with TYR 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C ALA* 4.3 12.6 - - + -
21C ASP 2.9 18.9 + - - -
22C HIS* 2.8 44.4 + + + -
24C PHE* 3.5 23.8 - + + -
58C ALA 2.8 16.8 + - - +
59C ALA 3.4 4.9 - - - +
61C GLY* 1.3 76.3 - - - +
63C ALA* 1.3 52.7 + - - +
65C CYS* 2.8 24.1 + - - +
66C LYS* 2.9 40.4 + - + +
68C PHE 3.3 22.2 - - - -
69C ALA* 3.8 7.2 - - + -
419C GLY 3.6 16.9 - - - +
422C THR* 4.0 2.2 - - + -
423C ALA* 3.6 26.7 - - + -
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Residues in contact with ALA 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C ALA 2.9 15.8 + - - +
60C ASP 3.6 0.2 - - - +
62C TYR* 1.3 76.6 - - - +
64C ARG* 1.3 59.1 + - - +
67C GLY* 2.7 30.9 + - - -
68C PHE* 3.7 21.5 - - - +
69C ALA* 3.7 11.4 - - + -
94C VAL* 3.4 28.0 - - + -
95C PRO* 4.0 10.8 - - + +
96C VAL* 4.3 0.4 - - + -
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Residues in contact with ARG 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C ASP* 2.9 32.4 + - - +
61C GLY* 3.1 9.1 + - - +
63C ALA* 1.3 76.9 - - - +
65C CYS* 1.3 59.6 + - - +
92C GLU* 2.9 32.1 + - - +
94C VAL* 3.9 12.7 - - + +
222C ARG* 3.3 37.1 - - - +
245C MET 5.8 1.8 + - - -
400C ASN* 3.3 15.3 + - - +
401C PHE 5.6 0.2 + - - -
402C ILE* 3.8 34.7 - - + +
403C VAL 2.8 27.6 + - - +
404C GLN* 4.1 9.1 - - - +
412C TYR* 3.2 13.6 + - - -
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Residues in contact with CYS 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C GLY 3.5 14.4 - - - -
62C TYR 2.8 8.7 + - - +
64C ARG* 1.3 83.2 - - - +
66C LYS* 1.3 60.7 + - - +
67C GLY 3.5 0.2 - - - -
378C ILE* 4.4 4.9 - - - -
400C ASN* 3.7 19.1 - - - -
402C ILE* 4.4 4.5 - - - -
420C ALA* 3.9 26.5 - - - -
423C ALA* 3.9 15.5 - - + -
424C CYS* 3.9 20.6 - - - -
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Residues in contact with LYS 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C CYS 5.2 0.5 - - - +
19C GLY* 3.8 24.1 - - - +
21C ASP* 2.4 34.0 + - - +
22C HIS* 4.9 4.2 + - - -
62C TYR* 2.9 44.5 + - + +
65C CYS* 1.3 79.8 - - + +
67C GLY* 1.3 60.0 + - - +
68C PHE* 3.2 6.0 + - - +
423C ALA* 3.7 29.5 + - + +
424C CYS* 5.7 1.3 - - - -
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Residues in contact with GLY 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C CYS 5.3 0.2 - - - -
63C ALA 2.7 24.1 + - - -
65C CYS 3.5 1.6 - - - -
66C LYS* 1.3 71.1 - - - +
68C PHE* 1.3 61.1 + - - +
95C PRO* 2.9 24.1 - - - +
160C ARG* 3.3 17.1 + - - -
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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