Contacts of the helix formed by residues 55 - 72 (chain D) in PDB entry 2OFJ
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 THR 55 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47D PRO* 3.8 4.3 - - - -
53D GLN 5.0 3.1 - - - +
54D GLU* 1.3 76.8 - - - +
56D TRP* 1.3 65.5 + - - +
57D GLU* 3.8 11.8 + - - +
58D GLU* 3.0 39.4 + - - +
59D ALA* 2.9 23.0 + - - +
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Residues in contact with TRP 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D ARG* 3.4 33.0 - - + -
9D TRP 3.8 13.7 - - - -
10D GLN* 3.4 32.5 - - + -
28D ASP* 3.4 44.6 - - + +
29D GLY* 3.3 19.2 + - - +
30D LEU* 3.8 20.4 - - + +
45D ILE 5.1 1.8 - - - -
47D PRO* 3.9 16.0 + - + +
55D THR* 1.3 73.2 - - - +
57D GLU* 1.3 79.6 + - + +
59D ALA* 3.5 3.1 - - - +
60D GLN* 2.9 29.0 + - - +
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Residues in contact with GLU 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D THR* 3.3 10.1 + - - +
56D TRP* 1.3 102.2 + - + +
58D GLU* 1.3 61.3 + - + +
60D GLN* 3.2 20.3 - - - +
61D SER* 2.9 26.5 + - - -
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Residues in contact with GLU 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D GLN 4.3 2.6 - - - +
54D GLU* 3.4 9.0 - - - +
55D THR* 3.0 42.6 + - - +
57D GLU* 1.3 75.3 - - + +
59D ALA* 1.3 58.9 + - - +
60D GLN 3.2 0.2 - - - -
61D SER* 3.3 6.6 + - - +
62D VAL* 2.9 32.9 + - - +
80D MET* 3.6 16.0 - - + +
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Residues in contact with ALA 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D LEU* 4.1 4.5 - - + -
45D ILE* 3.9 10.8 - - + -
47D PRO* 3.8 14.4 - - + -
55D THR 2.9 12.0 + - - +
56D TRP 3.5 9.4 - - - +
58D GLU* 1.3 75.1 - - - +
60D GLN* 1.3 53.7 + - - +
63D LEU* 2.7 38.3 + - - +
80D MET* 3.4 15.9 - - - -
82D SER* 3.7 23.1 - - - +
83D VAL* 3.6 2.9 - - + +
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Residues in contact with GLN 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D VAL* 5.9 0.4 - - + -
8D ARG* 3.1 44.5 + - - +
30D LEU* 3.7 25.1 - - + +
56D TRP* 2.9 19.7 + - - +
57D GLU* 3.2 26.9 - - - +
59D ALA* 1.3 76.5 - - - +
61D SER* 1.3 61.8 + - - +
63D LEU* 3.8 1.6 - - + +
64D LEU* 3.1 39.1 + - + +
319D LEU* 3.4 20.3 - - + +
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Residues in contact with SER 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57D GLU 2.9 13.7 + - - -
58D GLU* 3.3 8.9 + - - -
60D GLN* 1.3 77.5 - - - +
62D VAL* 1.3 66.8 + - - +
64D LEU* 3.3 6.0 + - - +
65D ALA* 3.1 24.1 + - - +
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Residues in contact with VAL 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D GLU 2.9 12.9 + - - +
59D ALA 4.1 0.7 - - - +
61D SER* 1.3 81.4 - - - +
63D LEU* 1.3 60.1 + - - +
65D ALA* 4.0 6.8 - - - +
66D TRP* 3.2 21.0 + - - +
78D PRO* 4.0 23.0 - - + +
80D MET* 3.5 33.4 - - + -
83D VAL* 3.8 17.7 - - + +
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Residues in contact with LEU 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D VAL* 4.0 33.2 - - + -
30D LEU* 4.1 19.7 - - + -
31D TYR 4.4 3.4 - - - +
32D VAL* 4.6 4.0 - - + -
45D ILE* 3.9 28.0 - - + -
59D ALA 2.7 22.4 + - - +
60D GLN* 3.8 4.0 - - - +
62D VAL* 1.3 72.6 - - - +
64D LEU* 1.3 61.7 + - - +
66D TRP* 2.9 5.7 + - + +
67D VAL* 2.8 36.7 + - + +
83D VAL* 4.0 13.7 - - + +
87D VAL* 3.8 28.3 - - + -
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Residues in contact with LEU 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D VAL* 3.6 36.3 - - + -
60D GLN* 3.1 32.5 + - + +
61D SER* 3.9 5.4 - - - +
63D LEU* 1.3 79.4 - - + +
65D ALA* 1.3 61.1 + - - +
67D VAL* 4.0 3.7 - - - +
68D ASN* 3.3 23.9 + - - +
319D LEU* 4.5 15.5 - - + -
320D LEU* 3.9 25.2 - - + +
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Residues in contact with ALA 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61D SER* 3.1 18.3 + - - +
62D VAL* 4.0 7.9 - - - +
64D LEU* 1.3 76.8 - - - +
66D TRP* 1.3 60.8 + - - +
68D ASN* 3.7 4.5 + - - +
69D ASN* 2.9 35.0 + - - +
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Residues in contact with TRP 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D LEU* 4.0 24.5 - - + -
62D VAL 3.2 16.1 + - - +
63D LEU* 2.9 6.9 + - - +
65D ALA* 1.3 77.7 - - - +
67D VAL* 1.3 78.3 + - + +
69D ASN* 3.1 10.0 + - + +
70D TRP* 2.9 58.7 + + + -
74D ASP 4.5 2.1 + - - -
75D CYS* 3.7 17.8 + - - -
76D GLU 2.7 31.6 + - - -
77D LEU* 3.8 3.6 - - - +
78D PRO* 3.6 23.1 - - + +
83D VAL* 4.7 5.6 - - + -
87D VAL* 3.3 42.6 - - + -
91D LEU* 4.0 7.4 - - + -
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Residues in contact with VAL 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D ALA* 3.4 28.3 - - + -
6D VAL* 4.0 16.6 - - + -
32D VAL* 4.0 27.1 - - + -
34D LEU* 4.7 1.3 - - + -
63D LEU* 2.8 25.9 + - + +
64D LEU* 4.0 4.7 - - - +
65D ALA 3.5 0.2 - - - -
66D TRP* 1.3 86.6 - - + +
68D ASN* 1.3 53.6 + - - +
70D TRP* 2.9 7.7 + - - +
71D LEU* 2.8 36.6 + - + +
320D LEU* 3.5 22.7 - - + -
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Residues in contact with ASN 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64D LEU 3.3 13.9 + - - +
65D ALA* 3.9 5.4 - - - +
66D TRP 3.3 0.6 - - - -
67D VAL* 1.3 80.8 - - - +
69D ASN* 1.3 59.2 + - - +
71D LEU* 3.2 18.0 + - - +
72D ALA* 3.1 23.9 + - - +
320D LEU* 4.2 19.0 - - - +
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Residues in contact with ASN 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D ALA* 2.9 26.7 + - - +
66D TRP* 3.1 10.3 + - + +
68D ASN* 1.3 77.1 - - - +
70D TRP* 1.3 56.9 + - - +
72D ALA* 3.3 9.5 + - - +
73D GLY 3.1 4.7 + - - -
74D ASP* 2.7 49.9 + - + +
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Residues in contact with TRP 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D ARG* 2.8 72.1 + - + +
3D SER 3.5 21.5 - - - -
4D ALA* 4.6 1.6 - - + -
34D LEU* 3.9 31.9 - - + -
35D ARG 3.5 22.0 - - - -
36D GLU* 4.2 4.4 + - - -
66D TRP* 2.9 42.3 + + + +
67D VAL 2.9 11.6 + - - +
69D ASN* 1.3 75.1 - - - +
71D LEU* 1.3 66.6 + - + +
73D GLY* 2.8 18.7 + - - -
74D ASP 3.1 14.9 + - - +
75D CYS* 4.2 7.1 - - + +
91D LEU* 3.5 17.8 - - + +
94D LEU* 3.5 22.2 - - + +
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Residues in contact with LEU 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D ARG* 3.2 52.5 - - + +
3D SER* 3.6 13.7 - - - +
4D ALA* 4.4 6.7 - - + +
67D VAL* 2.8 29.9 + - + +
68D ASN* 3.2 24.2 + - - +
70D TRP* 1.3 83.7 - - + +
72D ALA* 1.3 59.9 + - - +
73D GLY 3.3 1.0 + - - -
320D LEU* 4.8 10.1 - - + -
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Residues in contact with ALA 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D ASN 3.1 12.0 + - - +
69D ASN* 3.6 15.0 - - - +
70D TRP 3.1 0.4 - - - -
71D LEU* 1.3 75.0 - - - +
73D GLY* 1.3 57.5 + - - +
74D ASP* 3.6 2.5 - - + +
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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