Contacts of the helix formed by residues 53 - 67 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A LEU* 3.8 1.8 - - - -
51A PHE* 4.1 1.0 - - - +
52A THR* 1.3 100.4 + - - +
54A PRO* 1.3 72.2 - - - +
55A GLU* 4.0 1.8 - - - +
56A ALA* 3.1 10.6 + - + +
57A PHE* 3.0 21.1 + - - +
313A CL 3.4 16.9 - - + +
81D HIS* 4.0 30.0 - - + +
82D LEU* 3.8 33.6 - - + +
174D LYS* 5.1 7.8 + - - -
311D NAD 4.3 10.2 + - - -
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Residues in contact with PRO 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A LEU* 3.6 22.4 - - + -
34A PRO* 5.3 4.0 - - + -
52A THR 3.6 8.5 - - - +
53A GLU* 1.3 84.3 - - - +
55A GLU* 1.3 67.2 + - - +
57A PHE* 3.3 4.2 + - - +
58A GLU* 2.9 30.0 + - - +
89A MET* 4.5 2.8 - - - +
311A NAD 4.1 9.0 - - + +
54D PRO* 4.3 15.7 - - + -
55D GLU* 3.4 45.5 - - + +
311D NAD 5.5 0.4 - - - +
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Residues in contact with GLU 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A GLU* 3.9 0.3 - - - +
54A PRO* 1.3 85.6 - - - +
56A ALA* 1.3 58.0 + - - +
58A GLU* 3.4 10.1 + - - +
59A ALA* 3.0 23.2 + - - +
32D LEU* 3.9 1.0 - - - +
54D PRO* 3.5 22.5 - - + +
82D LEU* 3.8 9.8 - - + +
85D PRO* 3.5 35.6 - - + +
86D GLN* 2.9 22.7 + - + -
89D MET* 4.1 21.1 - - + -
92D ARG* 5.2 2.1 + - - +
311D NAD 2.5 35.6 + - - -
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Residues in contact with ALA 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A PHE* 3.8 19.1 - - + -
53A GLU* 3.1 17.0 + - + +
55A GLU* 1.3 76.7 - - - +
57A PHE* 1.3 65.9 + - - +
59A ALA* 3.3 3.8 + - - +
60A TYR* 3.0 25.1 + - - +
313A CL 4.0 11.7 - - + -
82D LEU* 5.6 0.2 - - + -
85D PRO* 3.8 17.2 - - + +
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Residues in contact with PHE 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A ALA* 3.7 8.5 - - + -
6A LEU 4.3 2.2 - - - -
7A THR* 4.1 4.5 - - + -
30A ALA* 4.1 8.3 - - + -
31A SER* 3.6 27.1 - - - -
32A LEU* 3.8 31.6 - - + -
51A PHE* 3.7 34.9 - + + -
53A GLU 3.0 11.6 + - - +
54A PRO 3.4 7.6 - - - +
56A ALA* 1.3 73.8 - - - +
58A GLU* 1.3 66.3 + - - +
60A TYR* 3.3 3.5 + - - +
61A LEU* 3.0 47.0 + - + +
74A LEU* 3.6 25.8 - - + -
89A MET* 3.9 25.1 - - + -
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Residues in contact with GLU 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A PRO 2.9 17.8 + - - +
55A GLU* 3.6 8.3 - - - +
57A PHE* 1.3 74.8 - - - +
59A ALA* 1.3 60.8 + - - +
61A LEU 3.2 1.0 + - - -
62A GLU* 2.8 30.5 + - - +
89A MET* 3.8 24.2 - - + +
92A ARG* 2.8 38.4 + - - +
93A LEU* 3.5 19.7 - - + +
55D GLU* 6.1 0.3 - - - +
58D GLU* 2.4 25.8 - - - +
89D MET* 4.8 2.6 - - - +
92D ARG* 3.1 25.9 + - - +
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Residues in contact with ALA 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A GLU 3.0 18.0 + - - +
56A ALA* 3.3 4.7 + - - +
58A GLU* 1.3 76.9 - - - +
60A TYR* 1.3 57.1 + - - +
62A GLU* 4.2 0.2 - - - -
63A ASP* 2.8 35.5 + - - +
84D TYR* 4.9 5.8 - - + -
85D PRO* 4.4 14.1 - - + -
88D ARG* 3.3 33.9 + - + +
92D ARG* 4.2 8.5 - - - +
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Residues in contact with TYR 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A VAL* 4.3 6.7 - - + +
30A ALA* 3.9 19.5 - - + -
49A GLU* 3.3 30.2 + - + +
51A PHE* 3.4 31.2 - + + -
56A ALA 3.0 17.5 + - - +
57A PHE 3.5 2.7 - - - +
59A ALA* 1.3 73.4 - - - +
61A LEU* 1.3 70.7 + - + +
63A ASP* 3.2 13.1 + - + +
64A LEU* 2.9 67.2 + - + +
67A ARG* 5.0 7.9 + - - -
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Residues in contact with LEU 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A ALA* 4.1 13.2 - - + -
30A ALA* 4.4 5.8 - - + -
57A PHE* 3.0 51.5 + - + +
58A GLU 3.8 0.2 - - - +
60A TYR* 1.3 91.0 - - + +
62A GLU* 1.3 57.1 + - - +
64A LEU* 3.4 13.4 + - + +
65A ARG* 3.0 26.2 + - - +
70A GLY* 5.0 2.3 - - - -
71A VAL* 4.0 36.5 + - + -
74A LEU* 4.7 4.3 - - + -
93A LEU* 3.7 33.5 - - + +
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Residues in contact with GLU 62 (chain A).
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 2.8 16.8 + - - +
61A LEU* 1.3 74.3 - - - +
63A ASP* 1.3 60.2 + - - +
65A ARG* 3.2 34.3 + - - +
66A ASP* 3.0 37.6 + - - +
93A LEU* 3.5 15.1 - - + +
88D ARG* 2.7 33.9 + - - +
92D ARG* 2.9 48.7 + - - +
116D LEU* 5.4 2.6 - - - +
119D ARG* 6.0 0.4 - - - -
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Residues in contact with ASP 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ALA* 2.8 19.5 + - - +
60A TYR* 3.2 14.2 + - + +
62A GLU* 1.3 75.7 - - - +
64A LEU* 1.3 61.8 + - - +
66A ASP* 3.2 4.0 + - - +
67A ARG* 3.2 38.8 + - - +
84D TYR* 4.5 4.7 + - - -
88D ARG* 2.8 33.7 + - - -
112D ARG* 2.9 23.6 + - - +
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Residues in contact with LEU 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A ARG* 4.1 3.1 - - - +
29A VAL* 3.9 20.6 - - + -
60A TYR* 2.9 53.7 + - + +
61A LEU* 3.5 19.3 - - + +
63A ASP* 1.3 68.2 - - - +
65A ARG* 1.3 68.2 + - - +
67A ARG* 3.1 46.1 + - - +
69A GLU* 2.9 48.8 + - + +
70A GLY* 3.7 4.9 - - - -
71A VAL* 4.8 3.4 - - + +
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Residues in contact with ARG 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A LEU 3.0 14.7 + - - +
62A GLU* 3.2 35.5 + - - +
64A LEU* 1.3 76.3 - - - +
66A ASP* 1.3 83.6 + - - +
68A GLY* 3.0 19.1 + - - -
70A GLY* 3.8 15.8 + - - +
92A ARG 3.3 24.7 + - - -
93A LEU* 3.4 27.9 - - - +
94A GLY* 4.7 4.7 - - - +
122A ARG* 6.2 0.4 - - - +
119D ARG* 4.3 6.9 - - - +
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Residues in contact with ASP 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A GLU* 3.0 19.2 + - - +
63A ASP 3.2 5.6 + - - +
65A ARG* 1.3 107.9 + - - +
67A ARG* 1.3 57.9 + - + +
68A GLY 3.4 0.8 + - - -
112D ARG* 2.8 26.4 + - - +
116D LEU* 4.7 0.3 - - - +
119D ARG* 2.7 33.7 + - - +
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Residues in contact with ARG 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A TYR* 5.0 9.5 + - - -
63A ASP* 3.2 28.2 + - - +
64A LEU* 3.1 37.3 + - - +
65A ARG 3.0 1.0 - - - -
66A ASP* 1.3 80.0 - - - +
68A GLY* 1.3 59.8 + - - +
69A GLU* 2.6 31.3 + - + +
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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