Contacts of the helix formed by residues 59 - 71 (chain E) in PDB entry 6OY5
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 59 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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696D HIS 2.8 29.0 + - - +
697D GLY 3.2 20.6 - - - -
698D LYS* 3.4 22.4 - - - +
756D GLN* 5.4 1.4 - - - +
760D ARG* 3.1 13.5 + - - +
57E ASP* 3.2 9.1 - - - +
58E PRO* 1.3 77.7 - - - +
60E ALA* 1.3 62.1 + - - +
61E VAL* 2.9 32.1 + - - +
62E THR* 3.1 18.2 + - - +
63E TRP* 3.2 23.7 + - - -
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Residues in contact with ALA 60 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
753D SER* 5.3 0.9 - - - +
27E ALA* 3.4 32.6 - - + +
30E LEU* 4.4 1.2 - - + +
31E LEU* 3.7 27.3 - - + +
35E PHE* 4.1 11.9 - - + -
58E PRO 3.2 4.6 + - - -
59E ASN* 1.3 71.4 + - - +
61E VAL* 1.3 62.0 + - + +
63E TRP* 3.4 9.5 - - - +
64E ALA* 2.8 29.6 + - - +
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Residues in contact with VAL 61 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
753D SER* 4.0 28.3 - - - +
756D GLN* 4.5 13.5 - - + -
757D ALA* 4.3 12.8 - - + +
760D ARG* 3.3 33.7 - - + +
761D ILE* 6.4 0.4 - - + -
23E VAL* 4.2 15.5 - - + -
24E ALA* 5.9 0.2 - - - -
27E ALA* 4.1 15.7 - - + -
59E ASN* 2.9 4.5 + - - +
60E ALA* 1.3 76.2 - - + +
62E THR* 1.3 65.2 + - - +
64E ALA* 3.3 2.6 + - - +
65E MET* 3.1 31.4 + - - +
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Residues in contact with THR 62 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
696D HIS* 5.8 0.2 - - - -
697D GLY* 4.6 4.0 - - - -
760D ARG* 3.2 22.0 + - - +
46E PRO* 4.7 9.0 - - + -
57E ASP* 3.2 28.1 + - - +
59E ASN* 3.1 18.3 + - - +
61E VAL* 1.3 80.1 - - - +
63E TRP* 1.3 64.0 + - - +
65E MET* 3.2 1.0 + - - -
66E LYS* 3.1 52.9 + - + +
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Residues in contact with TRP 63 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30E LEU* 3.8 14.4 - - + -
35E PHE* 3.9 32.9 - + - -
38E THR* 3.4 35.4 - - + -
40E LEU* 4.0 16.8 - - + -
45E ARG* 3.3 37.0 - - + -
46E PRO* 3.8 21.5 - - + -
56E ASP* 3.6 21.3 - - + -
57E ASP* 2.4 45.8 + - + +
59E ASN 3.2 21.6 + - - -
60E ALA* 3.4 9.2 - - - +
61E VAL 3.3 0.2 - - - -
62E THR* 1.3 79.7 - - - +
64E ALA* 1.3 58.4 + - - +
66E LYS* 3.1 2.3 + - - +
67E GLU* 2.8 35.2 + - - +
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Residues in contact with ALA 64 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23E VAL* 3.5 33.7 - - + +
26E ARG* 4.0 17.5 - - + +
27E ALA* 3.8 12.3 - - + +
30E LEU* 4.7 1.6 - - + -
60E ALA 2.8 21.1 + - - +
61E VAL 3.8 4.3 - - - +
62E THR 3.3 0.2 - - - -
63E TRP* 1.3 72.9 - - - +
65E MET* 1.3 64.0 + - - +
67E GLU* 3.8 4.1 - - - +
68E LEU* 3.1 25.5 + - - +
73E LEU* 4.8 1.7 - - - +
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Residues in contact with MET 65 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
760D ARG* 5.0 3.1 - - - -
761D ILE* 4.0 27.6 - - + -
3E GLU* 3.6 44.6 - - + +
4E PRO 5.4 2.5 - - - +
6E ILE* 4.1 6.3 - - + -
9E LEU* 3.6 28.3 - - + +
19E LEU* 5.4 0.4 - - + -
23E VAL* 3.8 22.7 - - + -
61E VAL* 3.1 25.6 + - - +
62E THR 3.9 2.9 - - - +
64E ALA* 1.3 77.4 - - - +
66E LYS* 1.3 72.7 + - + +
68E LEU* 3.2 9.5 + - - +
69E LEU* 3.1 26.1 + - + +
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Residues in contact with LYS 66 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
760D ARG* 4.8 0.4 - - - +
3E GLU* 3.5 22.6 + - - -
4E PRO* 3.7 33.1 + - - +
40E LEU* 4.5 9.0 - - + -
44E GLU 5.8 1.6 - - - +
46E PRO* 4.7 16.4 - - + -
62E THR* 3.1 35.6 + - + +
63E TRP* 3.1 9.8 + - - +
65E MET* 1.3 79.7 - - - +
67E GLU* 1.3 68.1 + - - +
69E LEU* 2.9 31.9 + - + +
70E THR* 3.4 10.3 + - - +
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Residues in contact with GLU 67 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26E ARG* 2.6 39.0 + - - +
30E LEU* 4.1 11.4 - - - +
38E THR* 2.5 33.3 + - - -
39E VAL* 3.0 19.5 + - + +
40E LEU* 3.7 26.8 - - + +
63E TRP* 2.8 23.3 + - + +
64E ALA 3.8 2.2 - - - +
66E LYS* 1.3 70.6 - - - +
68E LEU* 1.3 62.2 + - - +
70E THR* 2.6 27.2 + - - -
71E GLY 3.7 0.7 + - - -
72E ARG 4.5 1.6 + - - -
73E LEU* 3.6 15.5 - - + +
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Residues in contact with LEU 68 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1486D VAL* 5.0 0.4 - - + -
9E LEU* 4.1 10.5 - - + -
12E MET* 3.2 24.3 - - - +
19E LEU* 3.7 17.7 - - + -
22E VAL* 3.9 26.9 - - + -
23E VAL* 3.7 30.7 - - + +
26E ARG* 6.0 1.1 - - + -
64E ALA 3.1 10.8 + - - +
65E MET 3.3 10.1 - - - +
66E LYS 3.1 0.2 - - - -
67E GLU* 1.3 74.9 - - - +
69E LEU* 1.3 63.2 + - - +
71E GLY* 3.2 13.7 + - - -
73E LEU* 3.8 33.1 - - + +
75E PHE* 5.8 5.8 - - + -
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Residues in contact with LEU 69 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E PRO* 3.8 23.3 - - + +
5E GLY* 4.0 20.0 - - - +
8E LYS* 3.3 48.6 + - + +
9E LEU* 4.0 16.6 - - + -
12E MET* 3.8 4.0 - - - +
65E MET 3.1 16.5 + - - +
66E LYS* 2.9 23.2 + - + +
68E LEU* 1.3 76.4 - - - +
70E THR* 1.3 63.9 + - + +
71E GLY* 3.4 0.5 + - - -
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Residues in contact with THR 70 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E LYS* 5.6 0.2 + - - -
39E VAL* 4.1 1.4 - - - +
40E LEU* 3.8 12.1 - - + -
44E GLU* 4.5 3.8 - - - +
66E LYS 3.5 11.2 - - - +
67E GLU 2.6 19.9 + - - +
69E LEU* 1.3 78.1 - - + +
71E GLY* 1.3 59.2 + - - +
72E ARG* 3.0 61.7 + - - +
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Residues in contact with GLY 71 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1489D GLN* 5.8 0.5 - - - +
12E MET* 5.5 2.9 - - - -
67E GLU 3.7 0.2 + - - -
68E LEU 3.2 14.6 + - - -
69E LEU 3.3 0.9 - - - -
70E THR* 1.3 79.6 + - - +
72E ARG* 1.3 60.7 + - - +
73E LEU 3.2 16.5 + - - +
74E VAL* 5.8 0.9 - - - +
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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