Contacts of the helix formed by residues 47 - 65 (chain B) in PDB entry 3OTC
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 ASP 47 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B PHE* 3.5 11.6 - - + -
43B ALA* 2.8 37.4 + - - +
46B ASN* 1.3 74.4 - - - +
48B SER* 1.3 63.3 + - - +
49B ARG* 2.8 65.5 + - - +
50B ALA* 3.3 17.1 + - + +
51B LEU* 3.1 29.5 + - - +
116B PHE* 4.7 0.9 - - - -
206B TYR* 4.7 0.2 - - - -
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Residues in contact with SER 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B ASN 4.3 0.2 + - - -
47B ASP* 1.3 69.8 + - - +
49B ARG* 1.3 68.8 + - - +
51B LEU* 4.6 4.5 - - - +
52B GLN* 2.8 45.9 + - - +
203B LEU* 6.0 1.8 - - - -
205B MET* 5.3 3.6 - - - -
206B TYR* 3.5 26.5 + - - -
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Residues in contact with ARG 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B HIS 4.2 2.6 + - - -
41B ASN* 3.0 24.4 + - - +
42B PHE* 4.4 0.2 - - - +
43B ALA* 4.6 1.6 - - - +
47B ASP* 2.8 35.6 + - - +
48B SER* 1.3 75.9 - - - +
50B ALA* 1.3 59.5 + - - +
52B GLN* 5.0 2.0 - - - -
53B LEU* 3.2 21.7 + - - +
115B TYR* 3.5 38.3 - - - +
116B PHE* 3.4 38.3 - - + +
117B GLU 5.7 0.4 - - - +
118B ASP* 5.9 2.4 - - - +
119B GLN* 3.9 17.0 - - - +
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Residues in contact with ALA 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B PHE* 3.2 42.2 - - + -
47B ASP* 3.3 13.0 + - + +
48B SER 3.2 0.4 - - - -
49B ARG* 1.3 80.3 - - - +
51B LEU* 1.3 64.8 + - + +
53B LEU* 3.2 5.3 + - - +
54B MET* 3.1 28.4 + - + +
76B ASP* 5.8 1.6 - - - +
108B TYR* 5.2 3.7 - - - +
116B PHE* 3.5 10.7 - - + -
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Residues in contact with LEU 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B ASN* 4.5 8.1 - - + +
47B ASP 3.1 22.2 + - - +
48B SER 4.0 1.6 - - - +
50B ALA* 1.3 77.4 - - + +
52B GLN* 1.3 62.9 + - - +
54B MET* 3.4 8.0 + - + +
55B THR* 3.1 24.8 + - - -
73B GLY 5.9 0.9 - - - +
74B GLN* 4.8 1.8 - - - -
75B SER* 3.8 39.3 - - - +
78B TYR* 5.1 0.5 - - - -
205B MET* 4.3 24.5 - - + +
206B TYR* 3.7 35.0 - - + -
210B THR* 5.3 3.6 + - - +
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Residues in contact with GLN 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B SER* 2.8 30.7 + - - +
49B ARG* 5.3 0.3 - - - -
51B LEU* 1.3 73.7 - - - +
53B LEU* 1.3 65.5 + - - +
55B THR* 3.3 9.0 + - - -
56B LYS* 3.0 21.8 + - - +
115B TYR* 3.5 34.0 + - + -
205B MET* 4.3 28.7 - - + +
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Residues in contact with LEU 53 (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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49B ARG 3.2 14.1 + - - +
50B ALA 3.4 8.7 - - - +
52B GLN* 1.3 74.7 - - - +
54B MET* 1.3 66.0 + - - +
56B LYS* 3.0 4.7 + - + +
57B CYS* 3.0 31.1 + - - -
108B TYR* 3.3 48.7 - - + +
111B TYR* 3.7 38.8 - - + +
112B TRP* 3.5 25.4 - - + -
115B TYR* 3.8 17.2 - - + -
116B PHE* 4.0 7.4 - - + -
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Residues in contact with MET 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B LEU* 6.2 1.3 - - + -
33B PHE* 5.1 5.8 - - + -
50B ALA* 3.1 17.9 + - + +
51B LEU* 3.6 10.1 - - + +
52B GLN 3.4 0.2 - - - -
53B LEU* 1.3 79.1 - - - +
55B THR* 1.3 58.5 + - - +
57B CYS* 3.3 2.8 + - - -
58B ALA* 3.0 25.8 + - - +
75B SER 4.1 12.1 - - - +
76B ASP* 3.6 14.1 - - - +
77B GLU* 3.5 39.9 - - - +
78B TYR* 3.7 11.8 - - + -
104B PHE* 3.5 40.6 - - + -
108B TYR* 3.9 18.2 - - + +
127B PHE* 4.5 9.4 - - + -
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Residues in contact with THR 55 (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 LEU 3.1 13.3 + - - -
52B GLN* 3.6 11.0 - - - -
53B LEU 3.1 0.6 - - - -
54B MET* 1.3 79.9 - - - +
56B LYS* 1.3 56.2 + - - +
58B ALA* 3.2 1.6 + - - +
59B GLN* 2.8 39.1 + - + +
78B TYR* 2.9 27.6 + - - +
205B MET* 5.8 2.1 - - - +
210B THR* 3.8 21.7 + - + +
212B LEU* 3.8 23.8 - - + -
247B PRO* 4.1 12.1 - - + -
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Residues in contact with LYS 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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52B GLN 3.0 7.4 + - - +
53B LEU* 3.0 8.9 + - + +
55B THR* 1.3 76.9 - - - +
57B CYS* 1.3 62.0 + - - +
59B GLN* 3.3 22.6 + - + +
60B THR* 2.9 30.2 + - - -
63B GLU* 6.0 0.6 + - - -
111B TYR* 3.9 50.0 - - + -
114B ASP* 5.3 3.4 - - - -
115B TYR* 3.5 34.3 - - + +
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Residues in contact with CYS 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B LEU* 3.0 22.3 + - - -
54B MET 3.5 2.2 - - - +
56B LYS* 1.3 75.7 - - - +
58B ALA* 1.3 58.6 + - - +
60B THR* 3.1 5.9 + - - -
61B VAL* 2.9 30.3 + - - +
104B PHE* 3.4 30.5 - - + -
107B SER* 3.6 17.6 + - - -
108B TYR* 3.3 52.0 - - - -
111B TYR* 5.4 0.4 - - - -
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Residues in contact with ALA 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B MET 3.0 10.8 + - - +
55B THR 3.5 7.9 - - - +
57B CYS* 1.3 75.5 - - - +
59B GLN* 1.3 63.3 + - - +
61B VAL* 3.2 3.3 + - - +
62B MET* 3.0 27.4 + - - +
78B TYR* 3.4 38.8 - - + -
80B PHE* 3.5 19.7 - - + -
104B PHE* 3.4 2.0 - - + -
212B LEU* 3.6 8.5 - - + -
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Residues in contact with GLN 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 THR* 2.8 22.7 + - - +
56B LYS* 3.6 31.5 + - + +
57B CYS 3.2 0.2 - - - -
58B ALA* 1.3 76.3 - - - +
60B THR* 1.3 56.2 + - - +
62B MET* 3.2 5.7 + - - +
63B GLU* 2.8 40.6 + - - +
115B TYR* 5.5 0.3 + - - -
212B LEU* 3.9 18.4 - - + -
245B PRO* 2.8 39.3 + - + +
247B PRO* 3.6 20.8 - - - +
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Residues in contact with THR 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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124A PRO* 4.6 8.7 - - + -
56B LYS* 2.9 18.0 + - - +
57B CYS 3.1 5.4 + - - -
59B GLN* 1.3 74.7 - - - +
61B VAL* 1.3 64.8 + - - +
63B GLU* 3.4 13.2 + - - +
64B GLU* 3.0 40.2 + - + +
103B GLN* 3.9 15.0 - - + +
107B SER* 3.0 28.9 + - - +
111B TYR* 3.5 20.0 + - + +
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Residues in contact with VAL 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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57B CYS 2.9 16.8 + - - +
58B ALA 3.2 7.8 + - - +
60B THR* 1.3 76.0 - - - +
62B MET* 1.3 57.8 + - - +
65B LEU* 3.1 51.7 + - + +
68B ILE* 3.9 3.8 - - + +
80B PHE* 3.7 25.8 - - + -
100B VAL* 3.9 16.4 - - + +
103B GLN* 4.0 12.3 - - + -
104B PHE* 3.7 38.1 - - + +
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Residues in contact with MET 62 (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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58B ALA 3.0 12.3 + - - +
59B GLN* 3.2 9.8 + - - +
61B VAL* 1.3 79.6 - - - +
63B GLU* 1.3 59.5 + - - +
65B LEU 3.3 12.5 - - - +
66B GLU* 5.3 0.3 - - - -
68B ILE* 3.7 37.3 + - + +
69B VAL 4.3 4.7 - - - +
71B ALA* 3.7 22.2 - - + -
80B PHE* 4.3 4.9 - - + -
212B LEU* 3.8 36.1 - - - +
214B TRP* 3.2 56.7 - - + +
245B PRO* 4.0 17.7 - - + -
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Residues in contact with GLU 63 (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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56B LYS* 6.0 0.7 + - - -
59B GLN* 2.8 23.6 + - - +
60B THR* 4.0 14.7 + - - +
62B MET* 1.3 73.7 - - - +
64B GLU* 1.3 75.0 + - - +
65B LEU 3.7 4.0 - - - +
214B TRP* 4.1 11.3 - - + -
244B LYS* 4.1 23.4 + - - +
245B PRO* 4.1 21.1 - - + +
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Residues in contact with GLU 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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31A ARG* 3.3 25.9 + - - +
123A TYR* 5.8 6.1 - - - -
124A PRO 5.7 0.9 - - - +
60B THR* 3.0 29.3 + - + +
63B GLU* 1.3 88.2 - - + +
65B LEU* 1.3 64.3 + - + +
66B GLU* 4.8 2.4 - - - +
103B GLN* 3.8 35.6 + - + +
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Residues in contact with LEU 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ARG* 3.4 21.5 - - - +
61B VAL* 3.1 29.2 + - + +
62B MET 3.3 16.4 - - - +
63B GLU 3.7 4.2 - - - +
64B GLU* 1.3 83.4 - - + +
66B GLU* 1.3 67.9 + - - +
68B ILE* 4.2 8.3 - - + -
82B PHE* 4.4 6.1 - - + -
88B TRP* 3.7 27.1 - - + -
99B HIS* 3.9 20.2 - - + +
100B VAL* 3.5 42.0 - - + +
103B GLN* 5.2 5.2 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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