Contacts of the helix formed by residues 31 - 40 (chain N) in PDB entry 2DFS
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 31 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19N PHE* 3.8 12.6 - - + -
21N LYS* 2.6 36.0 + - - +
27N ILE* 4.3 13.7 - - + -
28N THR* 2.9 29.4 + - - +
30N LYS* 1.3 76.5 - - - +
32N LEU* 1.3 62.1 + - - +
33N GLY 3.3 2.0 - - - -
34N THR* 2.6 37.0 + - - +
35N VAL* 3.0 24.1 + - - +
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Residues in contact with LEU 32 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28N THR 3.8 2.0 + - - -
29N THR* 3.2 17.6 + - - +
30N LYS 3.3 0.4 - - - -
31N GLU* 1.3 77.4 - - - +
33N GLY* 1.3 60.3 + - - +
35N VAL* 3.3 9.5 - - + +
36N MET* 3.2 36.9 + - + +
48N LEU* 3.5 18.4 - - + +
51N MET* 5.2 2.7 - - + -
52N ILE* 3.5 32.5 - - + +
63N ILE* 3.4 30.7 - - + -
67N GLU* 5.2 4.7 - - - +
68N PHE* 3.7 28.7 - - + -
71N MET* 5.7 7.9 - - + -
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Residues in contact with GLY 33 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30N LYS 4.5 2.4 + - - -
31N GLU 3.3 0.6 - - - -
32N LEU* 1.3 78.5 - - - +
34N THR* 1.3 60.4 + - - +
36N MET* 3.8 3.6 + - - +
37N ARG* 3.2 47.0 + - - +
43N PRO* 5.4 0.4 - - - -
48N LEU* 3.4 34.0 - - - +
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Residues in contact with THR 34 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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783M MET* 3.7 39.2 - - + +
19N PHE* 3.7 11.2 - - - -
30N LYS 4.6 1.4 + - - -
31N GLU* 2.6 42.3 + - - +
33N GLY* 1.3 74.0 - - - +
35N VAL* 1.4 56.9 + - - -
37N ARG* 3.3 10.2 + - - +
38N SER* 2.9 28.4 + - - -
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Residues in contact with VAL 35 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15N ALA 4.6 7.4 - - - +
16N PHE* 4.6 7.2 - - + +
19N PHE* 3.6 31.5 - - + -
27N ILE* 3.9 18.8 - - + -
31N GLU 3.0 17.1 + - - +
32N LEU* 3.3 23.1 - - + +
34N THR* 1.4 71.5 - - - +
36N MET* 1.4 65.7 + - - +
38N SER* 3.1 3.3 + - - -
39N LEU* 3.1 26.3 + - + +
68N PHE* 3.5 39.0 - - + -
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Residues in contact with MET 36 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32N LEU* 3.2 40.4 + - + +
33N GLY 3.9 4.3 - - - +
35N VAL* 1.4 73.5 - - - +
37N ARG* 1.3 56.5 + - - +
39N LEU* 3.3 8.7 - - - +
40N GLY 3.2 28.4 + - - -
41N GLN* 3.5 24.8 + - - +
43N PRO* 3.9 24.7 - - + -
48N LEU* 3.7 22.0 - - - -
51N MET* 3.4 41.5 - - + +
68N PHE* 4.1 20.0 - - + -
71N MET* 5.3 1.1 - - + -
72N MET* 5.6 3.1 - - + +
79N THR* 5.3 1.1 - - + -
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Residues in contact with ARG 37 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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776M LYS 5.0 0.6 + - - -
779M ARG* 4.1 40.1 - - - +
780M GLY* 4.1 11.9 - - - +
783M MET* 4.1 20.2 - - + +
784M ARG* 3.7 19.2 - - - +
33N GLY* 3.2 36.3 + - - +
34N THR* 3.4 13.0 - - - +
35N VAL 3.3 0.2 - - - -
36N MET* 1.3 74.0 - - - +
38N SER* 1.3 57.4 + - - +
40N GLY 3.6 5.1 - - - +
41N GLN 3.2 20.4 - - - +
42N ASN* 4.3 4.2 - - - -
43N PRO* 2.7 40.0 + - + +
44N THR 3.2 15.8 + - - -
45N GLU* 2.6 31.3 + - - +
48N LEU* 4.8 1.0 - - - +
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Residues in contact with SER 38 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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783M MET* 5.8 2.0 - - - -
784M ARG* 4.9 8.0 - - - +
787M TYR* 3.8 43.3 - - - +
12N PHE* 5.8 0.3 - - - -
15N ALA* 5.0 9.5 - - - +
19N PHE* 3.4 29.0 - - - -
34N THR 2.9 15.0 + - - -
35N VAL* 3.1 7.4 + - - -
37N ARG* 1.3 77.2 - - - +
39N LEU* 1.3 64.7 + - - +
40N GLY* 3.5 0.7 - - - -
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Residues in contact with LEU 39 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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784M ARG* 5.5 1.1 - - - -
10N ALA* 3.0 42.2 - - + +
12N PHE* 3.6 52.3 - - + +
15N ALA* 4.1 12.1 - - + -
35N VAL* 3.1 9.4 + - + +
36N MET* 3.3 9.4 - - - +
38N SER* 1.3 78.7 - - - +
40N GLY* 1.3 56.9 + - - +
41N GLN* 4.6 14.4 - - - +
68N PHE* 4.2 23.3 - - + -
72N MET* 4.0 21.5 - - + -
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Residues in contact with GLY 40 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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780M GLY* 5.5 0.2 - - - -
784M ARG* 3.1 42.6 + - - -
10N ALA* 5.5 1.3 - - - -
36N MET 3.4 3.0 - - - +
37N ARG* 3.6 6.9 - - - -
38N SER 3.5 0.4 - - - -
39N LEU* 1.3 83.2 - - - +
41N GLN* 1.3 67.0 + - - +
42N ASN* 4.3 0.3 - - - +
83N GLU* 3.3 9.4 - - - -
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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