Contacts of the helix formed by residues 47 - 62 (chain B) in PDB entry 7CE1
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 GLY 47 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45B ASP 3.6 2.4 + - - -
46B ILE* 1.3 73.6 - - - +
48B ALA* 1.3 66.6 + - - -
49B GLU 3.2 3.6 - - - -
50B THR* 2.9 16.0 + - - -
51B LYS* 3.0 10.8 + - - +
3a T 3.7 26.8 - - - -
4a C 2.5 20.7 + - - -
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Residues in contact with ALA 48 (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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46B ILE 3.7 2.3 + - - -
47B GLY* 1.3 70.1 - - - +
49B GLU* 1.3 61.9 + - - +
51B LYS* 3.4 10.1 + - - +
52B GLU* 3.3 33.9 + - - +
3a T 5.1 3.6 + - - -
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Residues in contact with GLU 49 (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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47B GLY 3.1 1.0 + - - -
48B ALA* 1.3 75.6 - - - +
50B THR* 1.3 69.3 + - + +
52B GLU* 3.4 11.0 + - - +
53B ARG* 3.0 35.0 + - + +
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Residues in contact with THR 50 (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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31B LEU* 4.2 18.2 - - + -
35B THR* 5.1 0.2 - - - -
46B ILE* 3.4 8.6 - - - +
47B GLY 2.9 8.7 + - - -
49B GLU* 1.3 78.8 - - + +
51B LYS* 1.3 59.6 + - - +
53B ARG* 3.2 33.8 + - - +
54B VAL* 2.7 35.4 + - - +
4a C 2.5 45.9 + - - +
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Residues in contact with LYS 51 (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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39B ALA* 4.0 26.7 - - + +
42B ASP* 2.5 33.6 + - - +
43B ALA 2.7 33.7 + - - +
44B PRO* 4.8 1.0 - - - +
46B ILE* 3.2 22.6 + - + +
47B GLY 3.0 13.7 + - - +
48B ALA* 3.7 12.8 - - - +
49B GLU 3.2 0.2 - - - -
50B THR* 1.3 77.4 - - - +
52B GLU* 1.3 53.8 + - + +
54B VAL* 3.1 1.4 + - - +
55B ARG* 2.7 64.6 + - - +
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Residues in contact with GLU 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B ALA* 3.3 24.2 + - - +
49B GLU* 4.2 7.2 - - - +
51B LYS* 1.3 76.0 - - + +
53B ARG* 1.3 57.7 + - - +
55B ARG* 4.3 17.7 - - - +
56B LEU* 2.8 34.0 + - + +
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Residues in contact with ARG 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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29B THR* 2.6 38.1 + - + +
31B LEU* 3.7 20.6 - - - +
49B GLU* 3.0 29.1 + - + +
50B THR* 3.4 34.3 - - - +
52B GLU* 1.3 77.3 - - - +
54B VAL* 1.3 63.5 + - + +
56B LEU* 3.9 7.1 - - - +
57B ILE* 3.1 27.2 + - - +
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Residues in contact with VAL 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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25B ILE* 4.4 4.9 - - + -
29B THR* 4.9 5.6 - - + -
31B LEU* 3.7 26.7 - - + -
35B THR* 5.0 1.3 - - + +
36B VAL* 3.9 30.5 - - + +
39B ALA* 3.8 23.3 - - + -
40B LEU* 3.8 21.1 - - + -
50B THR* 2.7 23.5 + - - +
51B LYS 3.7 2.9 - - - +
53B ARG* 1.3 73.1 - - - +
55B ARG* 1.3 59.2 + - - +
57B ILE* 3.1 8.1 - - - +
58B ALA* 2.8 32.1 + - - +
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Residues in contact with ARG 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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39B ALA 4.3 13.5 + - - +
40B LEU* 4.0 28.0 - - + +
42B ASP* 3.7 15.2 + - - +
51B LYS* 2.7 60.6 + - - +
52B GLU* 4.3 14.6 - - - +
54B VAL* 1.3 73.0 - - - +
56B LEU* 1.3 62.7 + - - +
58B ALA* 4.0 0.6 - - - +
59B GLN* 3.2 25.3 + - - +
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Residues in contact with LEU 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 GLU 2.8 20.9 + - - +
53B ARG* 3.9 5.8 - - - +
55B ARG* 1.3 77.1 - - - +
57B ILE* 1.3 65.4 + - + +
59B GLN* 3.8 15.4 - - - +
60B GLN* 2.9 47.1 + - + +
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Residues in contact with ILE 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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25B ILE* 4.0 17.7 - - + +
28B MET* 3.5 50.0 - - + -
29B THR* 4.1 14.4 - - + -
53B ARG 3.1 15.5 + - - +
54B VAL* 3.1 21.3 - - - +
56B LEU* 1.3 78.6 - - + +
58B ALA* 1.3 61.1 + - - +
60B GLN* 3.3 7.7 + - + +
61B ILE* 3.1 35.0 + - + +
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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
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25B ILE* 4.0 19.7 - - + -
40B LEU* 3.9 24.7 - - + -
54B VAL 2.8 20.4 + - - +
55B ARG 4.0 3.4 - - - +
57B ILE* 1.3 77.9 - - - +
59B GLN* 1.3 56.7 + - - +
61B ILE* 3.4 5.9 - - - +
62B GLY* 3.0 6.8 - - - -
63B TYR* 2.7 34.6 + - + +
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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 ARG 3.2 17.7 + - - +
56B LEU* 3.8 15.6 - - - +
58B ALA* 1.3 78.2 - - - +
60B GLN* 1.3 82.2 + - - +
62B GLY* 3.5 9.7 - - - -
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Residues in contact with GLN 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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56B LEU* 2.9 40.3 + - + +
57B ILE* 3.6 8.7 - - + +
58B ALA 3.3 0.4 - - - -
59B GLN* 1.3 96.7 - - + +
61B ILE* 1.3 64.2 + - + +
62B GLY* 3.8 0.6 + - - -
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Residues in contact with ILE 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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20B PRO* 3.8 34.9 - - + +
25B ILE* 3.7 33.4 - - + -
28B MET* 4.1 27.6 - - + -
57B ILE* 3.1 26.9 - - + +
58B ALA 3.4 10.3 - - - +
60B GLN* 1.3 80.7 - - + +
62B GLY* 1.3 48.5 + - - -
63B TYR* 3.8 4.0 - - + +
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Residues in contact with GLY 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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132A GLU* 4.0 15.8 + - - +
20B PRO* 4.6 3.3 - - - +
58B ALA 3.0 15.3 - - - -
59B GLN* 3.5 12.1 - - - -
60B GLN 3.8 0.8 + - - -
61B ILE 1.3 71.7 + - - -
63B TYR* 1.3 65.2 + - - -
64B GLN* 3.6 10.9 + - - +
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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