Contacts of the helix formed by residues 53 - 67 (chain D) in PDB entry 3O9Z
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 GLU 53 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A HIS* 2.9 35.8 + - + +
82A LEU* 3.9 32.2 - - + +
174A LYS* 4.3 11.8 + - - -
311A NAD 4.6 7.7 + - - -
32D LEU* 3.8 2.5 - - - -
51D PHE* 3.5 1.1 - - - +
52D THR* 1.3 91.6 + - - +
54D PRO* 1.3 71.2 - - - +
55D GLU* 4.0 1.9 - - - +
56D ALA* 3.0 17.3 + - + +
57D PHE* 3.0 13.0 + - - +
313D CL 3.4 18.7 - - + +
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Residues in contact with PRO 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A PRO* 4.3 16.6 - - + -
55A GLU* 3.5 45.3 - - + +
311A NAD 5.9 0.2 - - - +
32D LEU* 3.8 19.5 - - + -
52D THR 3.5 8.7 - - - +
53D GLU* 1.3 85.3 - - - +
55D GLU* 1.3 66.2 + - + +
57D PHE* 3.3 3.3 + - + +
58D GLU* 2.9 29.6 + - - +
89D MET* 4.3 5.5 - - + +
311D NAD 3.8 9.9 - - + +
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Residues in contact with GLU 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 4.0 0.5 - - - +
54A PRO* 3.4 28.9 - - + +
58A GLU* 6.1 0.2 - - - +
82A LEU* 3.8 13.6 - - + +
85A PRO* 3.4 35.9 - - + +
86A GLN* 2.8 35.2 + - + +
89A MET* 4.4 15.5 - - + -
92A ARG* 5.0 2.5 + - - +
311A NAD 2.9 15.2 + - - -
53D GLU* 3.8 0.7 - - - +
54D PRO* 1.3 88.1 - - - +
56D ALA* 1.3 57.3 + - - +
58D GLU* 3.8 9.4 - - - +
59D ALA* 3.0 23.0 + - - +
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Residues in contact with ALA 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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81A HIS* 6.4 0.7 - - + -
82A LEU* 5.6 0.2 - - + -
85A PRO* 3.8 18.7 - - + +
51D PHE* 3.7 20.3 - - + -
53D GLU* 3.0 16.9 + - + +
55D GLU* 1.3 76.5 - - - +
57D PHE* 1.3 65.3 + - - +
59D ALA* 3.3 2.9 + - - +
60D TYR* 3.0 24.9 + - - +
313D CL 4.0 11.2 - - + -
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Residues in contact with PHE 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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5D ALA* 3.8 4.9 - - + -
6D LEU 4.2 5.6 - - - -
7D THR* 4.0 12.1 - - + -
30D ALA* 4.0 9.2 - - + -
31D SER* 3.7 25.8 - - - -
32D LEU* 3.8 28.7 - - + -
51D PHE* 3.7 35.1 - + + -
53D GLU 3.0 11.3 + - - +
54D PRO 3.4 8.3 - - - +
56D ALA* 1.3 75.5 - - - +
58D GLU* 1.3 62.1 + - - +
60D TYR* 3.2 3.5 + - - +
61D LEU* 3.0 52.4 + - + +
74D LEU* 3.7 24.9 - - + -
89D MET* 3.9 20.0 - - - -
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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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58A GLU* 2.4 26.1 - - - +
89A MET* 5.7 0.2 - - - +
92A ARG* 3.3 23.6 + - - +
54D PRO 2.9 16.0 + - - +
55D GLU* 3.4 8.7 + - - +
57D PHE* 1.3 76.8 - - - +
59D ALA* 1.3 57.0 + - - +
61D LEU* 3.2 6.5 + - - +
62D GLU* 2.8 27.9 + - - +
89D MET* 3.6 30.9 - - + +
92D ARG* 2.8 42.7 + - - +
93D LEU* 3.8 9.4 - - + +
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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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84A TYR* 4.7 7.2 - - + -
85A PRO* 4.2 14.6 - - + -
88A ARG* 3.2 30.9 + - + +
92A ARG* 4.0 10.7 - - - +
55D GLU 3.0 17.0 + - - +
56D ALA* 3.8 4.5 - - - +
57D PHE 3.3 0.4 - - - -
58D GLU* 1.3 77.0 - - - +
60D TYR* 1.3 55.6 + - - +
63D ASP* 2.9 36.6 + - - -
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Residues in contact with TYR 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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29D VAL* 4.0 12.0 - - + +
30D ALA* 3.9 20.0 - - + -
49D GLU* 3.4 30.5 + - + +
51D PHE* 3.5 35.2 - + + -
56D ALA 3.0 11.0 + - - +
57D PHE 3.5 3.1 - - - +
58D GLU 3.2 0.2 - - - -
59D ALA* 1.3 75.4 - - - +
61D LEU* 1.3 74.1 + - + +
63D ASP* 3.3 12.8 + - + +
64D LEU* 3.1 52.8 + - + +
67D ARG* 5.7 4.0 + - - -
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Residues in contact with LEU 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D ALA* 4.2 13.9 - - + -
29D VAL* 5.2 0.2 - - + -
30D ALA* 4.5 5.4 - - + -
57D PHE* 3.0 54.0 + - + +
58D GLU* 3.7 1.1 - - - +
60D TYR* 1.3 93.9 - - + +
62D GLU* 1.3 57.3 + - - +
64D LEU* 3.3 12.0 + - + +
65D ARG* 2.9 27.0 + - - +
70D GLY* 4.8 1.7 - - - -
71D VAL* 4.0 34.3 + - + +
74D LEU* 4.7 3.6 - - + -
93D LEU* 3.7 34.7 - - + +
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Residues in contact with GLU 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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88A ARG* 2.7 34.8 + - - +
92A ARG* 2.8 49.0 + - - +
116A LEU* 5.1 5.0 - - - +
119A ARG* 6.0 0.2 - - - -
58D GLU 2.8 16.6 + - - +
60D TYR 3.2 0.2 - - - -
61D LEU* 1.3 74.3 - - - +
63D ASP* 1.3 59.0 + - - +
65D ARG* 3.3 32.6 + - - +
66D ASP* 2.9 39.9 + - - +
92D ARG* 6.0 0.5 - - - +
93D LEU* 3.5 13.8 - - + +
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Residues in contact with ASP 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A TYR* 4.5 4.7 + - - -
88A ARG* 2.8 31.9 + - - -
112A ARG* 5.4 11.2 - - - +
59D ALA* 2.9 18.5 + - - +
60D TYR* 3.4 14.8 - - + +
62D GLU* 1.3 76.4 - - - +
64D LEU* 1.3 61.9 + - + +
66D ASP* 3.3 8.4 + - - +
67D ARG* 3.2 40.3 + - - +
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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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3D ARG* 4.0 11.0 - - - +
29D VAL* 3.8 20.2 - - + -
60D TYR* 3.1 49.6 + - + +
61D LEU* 3.5 17.0 - - + +
62D GLU 3.2 0.2 - - - -
63D ASP* 1.3 77.0 - - - +
65D ARG* 1.3 66.4 + - - +
67D ARG* 3.2 43.5 + - - +
68D GLY 3.3 0.2 + - - -
69D GLU* 2.9 41.4 + - + +
70D GLY* 3.7 4.9 - - - -
71D VAL* 4.9 4.0 - - + +
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Residues in contact with ARG 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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119A ARG* 4.6 5.5 - - - +
61D LEU 2.9 14.0 + - - +
62D GLU* 3.5 38.7 + - - +
64D LEU* 1.3 76.0 - - - +
66D ASP* 1.3 83.3 + - - +
68D GLY* 3.0 20.1 + - - -
70D GLY* 3.7 16.5 - - - +
92D ARG 3.0 26.1 + - - -
93D LEU* 3.5 30.7 - - - +
94D GLY* 4.7 2.9 - - - +
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Residues in contact with ASP 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ARG* 4.8 2.1 + - - -
116A LEU* 4.5 5.2 - - - +
119A ARG* 2.5 40.7 + - - +
62D GLU* 2.9 26.3 + - - +
63D ASP* 3.3 9.2 + - - +
65D ARG* 1.3 108.5 + - - +
67D ARG* 1.3 57.5 + - + +
68D GLY 3.3 1.9 + - - -
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Residues in contact with ARG 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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112A ARG* 6.1 3.7 - - - +
60D TYR* 5.7 4.2 + - - -
63D ASP* 3.2 31.9 + - - +
64D LEU* 3.5 34.4 - - - +
65D ARG 3.2 0.8 - - - -
66D ASP* 1.3 76.3 - - - +
68D GLY* 1.3 60.8 + - - +
69D GLU* 3.4 28.5 + - + +
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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