Contacts of the helix formed by residues 53 - 66 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32B LEU* 3.7 2.6 - - - +
51B PHE* 3.5 1.2 - - - +
52B THR* 1.3 96.9 + - - +
54B PRO* 1.3 70.9 - - - +
55B GLU* 3.9 1.7 - - - +
56B ALA* 3.0 17.8 + - + +
57B PHE* 3.0 12.8 + - - +
314B EDO 4.0 1.7 - - - -
315B CL 3.4 18.0 - - + +
81C HIS* 3.3 34.6 - - + +
82C LEU* 3.8 32.5 - - + +
174C LYS* 4.5 9.2 + - - -
311C NAD 4.5 8.1 + - - -
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Residues in contact with PRO 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B LEU* 3.7 22.2 - - + -
34B PRO* 5.7 2.7 - - + -
52B THR 3.6 9.0 - - - +
53B GLU* 1.3 84.5 - - - +
55B GLU* 1.3 66.1 + - - +
57B PHE* 3.3 2.8 + - + +
58B GLU* 2.9 31.6 + - - +
89B MET* 4.1 5.6 - - + +
311B NAD 4.1 8.3 - - - +
54C PRO* 4.4 15.7 - - + -
55C GLU* 3.3 45.5 - - + +
311C NAD 6.0 0.2 - - - +
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Residues in contact with GLU 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B GLU* 3.9 0.9 - - - +
54B PRO* 1.3 88.3 - - - +
56B ALA* 1.3 57.2 + - - +
58B GLU* 3.6 12.9 + - - +
59B ALA* 3.1 22.2 + - - +
32C LEU* 4.1 0.2 - - - +
54C PRO* 3.4 26.6 - - + +
82C LEU* 3.7 13.5 - - + +
85C PRO* 3.5 35.0 - - + +
86C GLN* 2.8 36.0 + - + -
89C MET* 4.1 16.2 - - + -
92C ARG* 5.4 2.5 + - - +
311C NAD 2.8 16.3 + - - -
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Residues in contact with ALA 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B PHE* 3.8 18.8 - - + -
53B GLU* 3.0 16.2 + - + +
55B GLU* 1.3 76.8 - - - +
57B PHE* 1.3 65.2 + - - +
59B ALA* 3.3 3.3 + - - +
60B TYR* 3.0 25.1 + - - +
315B CL 3.9 11.9 - - + -
81C HIS 6.1 0.2 - - - +
85C PRO* 3.9 16.2 - - + +
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Residues in contact with PHE 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B ALA* 3.8 5.4 - - + -
6B LEU 4.2 5.4 - - - -
7B THR* 4.0 8.3 - - + -
30B ALA* 4.1 8.7 - - + -
31B SER* 3.6 26.2 - - - -
32B LEU* 3.7 32.8 - - + -
51B PHE* 3.7 34.3 - + + -
53B GLU 3.0 11.6 + - - +
54B PRO 3.4 7.6 - - - +
56B ALA* 1.3 79.1 - - - +
58B GLU* 1.3 58.0 + - - +
60B TYR* 3.3 2.4 + - - +
61B LEU* 3.0 55.4 + - + +
74B LEU* 3.7 28.3 - - + -
89B MET* 4.1 17.0 - - - -
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Residues in contact with GLU 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B PRO 2.9 16.0 + - - +
55B GLU* 3.6 12.6 - - - +
57B PHE* 1.3 75.9 - - - +
59B ALA* 1.3 57.0 + - - +
61B LEU 3.2 0.9 + - - -
62B GLU* 3.0 31.0 + - - +
89B MET* 3.4 29.3 - - + +
92B ARG* 2.4 43.0 + - - +
93B LEU* 3.6 22.1 - - + +
58C GLU* 2.5 22.4 - - - +
89C MET* 5.1 0.5 - - - +
92C ARG* 3.0 24.2 + - - +
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Residues in contact with ALA 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B GLU 3.1 14.5 + - - +
56B ALA* 3.8 6.5 - - - +
57B PHE 3.2 0.2 - - - -
58B GLU* 1.3 78.7 - - - +
60B TYR* 1.3 58.8 + - - +
62B GLU* 3.4 3.7 + - - -
63B ASP* 2.9 37.0 + - - +
84C TYR* 4.9 5.8 - - + -
85C PRO* 4.5 9.2 - - + -
88C ARG* 3.5 35.2 + - - +
92C ARG* 4.9 5.1 - - - +
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Residues in contact with TYR 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B VAL* 4.4 5.9 - - + +
30B ALA* 4.0 18.4 - - + -
49B GLU* 3.3 30.2 + - + +
51B PHE* 3.4 38.1 - + + -
56B ALA 3.0 11.7 + - - +
57B PHE 3.5 2.5 - - - +
59B ALA* 1.3 76.7 - - - +
61B LEU* 1.3 68.4 + - + +
63B ASP* 3.2 13.0 + - + +
64B LEU* 3.0 66.8 + - + +
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Residues in contact with LEU 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B ALA* 4.3 11.7 - - + -
30B ALA* 4.5 6.5 - - + -
57B PHE* 3.0 51.6 + - + +
58B GLU 3.2 0.6 + - - +
60B TYR* 1.3 89.9 - - + +
62B GLU* 1.3 61.1 + - - +
64B LEU* 3.3 12.7 + - + +
65B ARG* 2.9 28.8 + - - +
70B GLY* 4.9 1.9 - - - -
71B VAL* 4.1 36.7 - - + +
74B LEU* 4.7 4.5 - - + -
93B LEU* 3.8 32.2 - - + +
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Residues in contact with GLU 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B GLU* 3.0 16.6 + - - +
59B ALA* 3.5 4.2 - - - +
61B LEU* 1.3 75.4 - - - +
63B ASP* 1.3 55.6 + - - +
65B ARG* 3.1 34.3 + - - +
66B ASP* 2.5 47.8 + - - +
93B LEU* 3.4 13.7 - - + +
88C ARG* 3.1 19.8 + - - +
92C ARG* 3.5 36.6 + - - +
116C LEU* 5.8 3.1 - - - +
119C ARG* 5.3 4.2 + - - -
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Residues in contact with ASP 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B ALA* 2.9 17.6 + - - +
60B TYR* 3.2 15.0 + - + +
62B GLU* 1.3 77.0 - - - +
64B LEU* 1.3 61.4 + - + +
66B ASP* 3.9 8.0 - - - +
67B ARG* 3.3 38.8 + - - +
88C ARG* 2.9 29.6 + - - -
112C ARG* 3.3 30.0 + - - -
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Residues in contact with LEU 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B ARG* 4.2 2.0 - - - +
29B VAL* 3.8 22.4 - - + -
60B TYR* 3.0 59.7 + - + +
61B LEU* 3.5 18.2 - - + +
62B GLU 3.2 0.2 - - - -
63B ASP* 1.3 77.0 - - + +
65B ARG* 1.3 57.9 + - - +
67B ARG* 3.4 26.9 + - - +
68B GLY 3.3 4.2 + - - -
69B GLU* 2.8 54.8 + - + +
70B GLY* 3.8 4.5 - - - -
71B VAL* 4.6 4.0 - - + -
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Residues in contact with ARG 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B LEU 2.9 16.1 + - - +
62B GLU* 3.5 31.7 + - - +
64B LEU* 1.3 71.9 - - - +
66B ASP* 1.3 94.1 + - - +
67B ARG 2.7 14.9 + - - -
68B GLY* 3.1 11.8 + - - -
70B GLY* 3.9 15.0 - - - +
92B ARG* 3.6 20.6 + - - +
93B LEU* 3.5 32.5 + - - +
94B GLY* 4.8 4.0 - - - +
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Residues in contact with ASP 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B GLU* 2.5 40.9 + - - +
63B ASP* 3.9 7.7 - - - +
65B ARG* 1.3 106.6 + - - +
67B ARG* 1.3 59.0 + - - +
88C ARG* 4.7 4.3 + - - -
116C LEU* 5.4 2.9 - - - +
119C ARG* 4.2 29.6 + - - +
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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