Contacts of the helix formed by residues 31 - 40 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19B PHE* 3.7 15.4 - - + -
21B LYS* 2.6 37.2 + - - -
27B ILE* 4.3 12.8 - - + -
28B THR* 2.9 33.6 + - - +
30B LYS* 1.3 76.0 - - + +
32B LEU* 1.4 62.9 + - - +
33B GLY 3.4 2.2 - - - -
34B THR* 3.0 14.6 + - - +
35B VAL* 3.0 23.6 + - - +
94C LYS* 4.3 14.6 + - - +
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Residues in contact with LEU 32 (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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28B THR 3.8 2.4 + - - -
29B THR 3.2 16.8 + - - +
30B LYS 3.3 0.4 - - - -
31B GLU* 1.4 77.2 - - - +
33B GLY* 1.3 62.2 + - - +
35B VAL* 3.3 10.4 - - + +
36B MET* 3.1 37.8 + - + +
48B LEU* 3.5 17.7 - - + +
51B MET* 5.2 3.6 - - + -
52B ILE* 3.5 31.6 - - + +
63B ILE* 3.4 31.6 - - + -
67B GLU* 5.2 4.3 - - - +
68B PHE* 3.7 28.0 - - + -
71B MET* 5.7 8.1 - - + -
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Residues in contact with GLY 33 (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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30B LYS 4.5 2.4 + - - -
31B GLU* 3.4 1.0 - - - +
32B LEU* 1.3 77.9 - - - +
34B THR* 1.3 58.9 + - - +
36B MET* 3.8 4.0 + - - +
37B ARG* 3.2 47.9 + - - +
48B LEU* 3.3 34.0 - - - +
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Residues in contact with THR 34 (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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783A MET* 3.8 34.7 - - + +
19B PHE* 3.7 18.6 - - - -
30B LYS 4.8 1.1 + - - -
31B GLU* 3.0 26.7 + - - +
33B GLY* 1.3 74.8 - - - +
35B VAL* 1.4 57.4 + - - +
37B ARG* 3.3 10.5 + - + +
38B SER* 2.9 28.9 + - - -
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Residues in contact with VAL 35 (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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15B ALA* 4.6 8.7 - - + +
16B PHE* 4.6 6.7 - - + +
19B PHE* 3.8 31.5 - - + -
27B ILE* 4.0 19.1 - - + -
31B GLU 3.0 15.8 + - - +
32B LEU* 3.3 23.1 - - + +
34B THR* 1.4 71.2 + - - +
36B MET* 1.4 65.7 + - - +
38B SER* 3.1 2.4 + - - -
39B LEU* 3.0 27.3 + - + +
68B PHE* 3.5 39.3 - - + -
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Residues in contact with MET 36 (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* 3.1 37.6 + - + +
33B GLY 3.9 1.8 - - - +
35B VAL* 1.4 73.9 - - - +
37B ARG* 1.3 56.3 + - - +
39B LEU* 3.3 8.9 - - - +
40B GLY 3.1 22.5 + - - -
41B GLN* 3.4 30.7 + - - +
43B PRO* 3.8 28.3 - - + -
48B LEU* 3.7 22.7 - - - -
51B MET* 3.4 41.3 - - + +
68B PHE* 4.1 18.8 - - + -
71B MET* 5.3 1.6 - - + -
72B MET* 5.6 3.1 - - + +
79B THR* 5.4 0.9 - - + -
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Residues in contact with ARG 37 (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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779A ARG* 3.9 39.7 - - - +
780A GLY* 4.2 4.8 - - - +
783A MET* 3.6 31.6 - - + +
784A ARG* 4.1 10.9 - - - +
33B GLY* 3.2 35.6 + - - +
34B THR* 3.3 12.8 + - - +
35B VAL 3.3 0.6 - - - -
36B MET* 1.3 73.7 - - - +
38B SER* 1.3 57.1 + - - +
40B GLY 3.9 7.8 - - - +
41B GLN 3.2 19.7 - - - +
42B ASN* 4.3 3.3 - - - -
43B PRO* 2.7 39.8 + - + +
44B THR 3.1 16.0 + - - -
45B GLU* 2.6 30.7 + - - +
48B LEU* 4.7 0.8 - - - +
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Residues in contact with SER 38 (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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783A MET* 5.5 2.9 - - - -
784A ARG* 5.1 6.8 - - - +
787A TYR* 3.8 42.9 - - - +
12B PHE* 5.8 0.3 - - - -
15B ALA* 4.9 10.0 - - - +
19B PHE* 3.4 28.8 - - - -
34B THR 2.9 15.0 + - - -
35B VAL* 3.1 6.7 + - - -
37B ARG* 1.3 75.9 - - - +
39B LEU* 1.3 64.6 - - - +
40B GLY* 3.5 0.4 - - - -
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Residues in contact with LEU 39 (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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784A ARG* 4.8 2.1 + - - -
10B ALA* 3.0 42.0 - - + +
11B GLU* 4.3 0.2 - - - -
12B PHE* 3.6 53.5 - - + +
15B ALA* 4.2 11.9 - - + -
16B PHE 5.6 0.2 - - - +
35B VAL* 3.0 10.3 + - + +
36B MET* 3.3 10.3 - - - +
38B SER* 1.3 77.8 - - - +
40B GLY* 1.3 56.4 + - - +
41B GLN* 4.5 14.4 - - - +
68B PHE* 4.1 22.4 - - + -
72B MET* 4.0 20.6 - - + -
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Residues in contact with GLY 40 (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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780A GLY* 5.0 0.9 - - - -
784A ARG* 3.1 41.7 + - - -
10B ALA* 5.6 2.7 - - - -
36B MET 3.1 1.8 + - - +
37B ARG* 3.9 7.3 - - - +
38B SER 3.5 0.8 - - - -
39B LEU* 1.3 83.8 - - - +
41B GLN* 1.3 67.9 + - - +
42B ASN* 4.1 1.6 - - - +
83B GLU* 3.1 12.8 - - - -
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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