Contacts of the helix formed by residues 35 - 51 (chain B) in PDB entry 2FAC
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 35 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33B GLY 3.3 3.9 + - - +
34B ALA* 1.3 75.7 - - - +
36B SER* 1.3 66.0 + - - +
37B LEU* 3.2 10.3 + - - +
38B ASP* 2.8 44.2 + - - +
39B THR* 3.1 21.7 + - - +
302B PM4 4.6 2.2 - - - -
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Residues in contact with SER 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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35B ASP* 1.3 76.0 - - - +
37B LEU* 1.3 61.0 + - - +
39B THR* 2.9 18.9 + - - -
40B VAL* 3.5 11.8 + - - +
302B PM4 1.6 63.7 + - - -
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Residues in contact with LEU 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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35B ASP* 3.2 7.4 + - - +
36B SER* 1.3 76.3 - - - +
38B ASP* 1.3 70.0 + - - +
40B VAL* 3.0 15.9 + - + +
41B GLU* 2.9 51.3 + - + +
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Residues in contact with ASP 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B GLN* 4.8 5.6 - - - +
15B LEU* 3.6 25.6 - - + +
33B GLY 3.7 4.5 - - - +
34B ALA* 3.5 6.6 - - - -
35B ASP* 2.8 58.2 + - - +
37B LEU* 1.3 77.8 - - - +
39B THR* 1.3 57.6 + - - +
41B GLU* 3.2 14.5 + - - +
42B LEU* 2.8 30.3 + - - +
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Residues in contact with THR 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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28B PHE* 5.3 0.2 - - + -
29B VAL* 4.3 3.8 - - + -
34B ALA* 3.8 18.2 - - + -
35B ASP 3.1 10.9 + - - +
36B SER 2.9 15.8 + - - -
37B LEU 3.1 0.2 - - - -
38B ASP* 1.3 76.9 - - - +
40B VAL* 1.3 65.7 + - - +
42B LEU* 3.3 8.0 + - + +
43B VAL* 3.0 29.6 + - - +
302B PM4 3.0 63.2 + - - +
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Residues in contact with VAL 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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36B SER 3.5 11.4 + - - +
37B LEU* 3.0 22.0 + - + +
39B THR* 1.3 83.6 + - - +
41B GLU* 1.3 63.6 + - + +
43B VAL* 3.4 6.6 + - - +
44B MET* 3.1 48.0 + - + +
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Residues in contact with GLU 41 (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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14B GLN* 3.4 22.5 + - - +
37B LEU* 2.9 47.8 + - + +
38B ASP* 3.7 15.5 - - - +
40B VAL* 1.3 77.5 - - + +
42B LEU* 1.3 60.6 + - - +
44B MET* 3.4 9.4 + - - +
45B ALA* 2.9 28.2 + - - +
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Residues in contact with LEU 42 (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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10B ILE* 4.3 5.4 - - + -
11B ILE* 4.0 22.7 - - + -
14B GLN* 3.5 31.1 - - + +
15B LEU* 4.7 13.0 - - + -
28B PHE* 3.7 39.5 - - + -
38B ASP 2.8 21.4 + - - +
39B THR* 3.7 7.4 - - - +
41B GLU* 1.3 70.6 - - - +
43B VAL* 1.3 67.8 + - - +
45B ALA 3.2 0.5 + - - -
46B LEU* 3.0 35.8 + - + +
302B PM4 4.3 13.9 - - + +
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Residues in contact with VAL 43 (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 THR 3.0 21.6 + - - +
40B VAL* 3.6 7.2 - - - +
42B LEU* 1.3 76.1 - - - +
44B MET* 1.3 64.3 + - + +
46B LEU* 3.2 3.5 + - - +
47B GLU* 3.0 44.1 + - - +
54B ILE* 3.7 17.9 - - + -
59B ALA* 4.0 10.5 - - + -
302B PM4 3.6 43.5 - - + +
409B ZN 4.4 13.0 - - - -
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Residues in contact with MET 44 (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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40B VAL* 3.1 36.9 + - + +
41B GLU* 3.7 8.3 - - - +
42B LEU 3.3 0.2 - - - -
43B VAL* 1.3 78.6 - - + +
45B ALA* 1.3 62.8 + - - +
47B GLU* 3.3 16.4 + - - +
48B GLU* 3.0 23.6 + - - +
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Residues in contact with ALA 45 (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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10B ILE* 3.9 20.6 - - + +
14B GLN* 3.7 21.1 - - + +
41B GLU 2.9 16.7 + - - +
42B LEU 3.7 4.9 - - - +
43B VAL 3.2 0.2 - - - -
44B MET* 1.3 77.0 - - - +
46B LEU* 1.3 57.9 + - - +
48B GLU* 3.4 8.0 + - - +
49B GLU* 3.1 28.1 + - - +
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Residues in contact with LEU 46 (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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7B VAL* 4.4 19.1 - - + +
10B ILE* 4.0 21.5 - - + -
11B ILE* 5.1 2.7 - - + -
42B LEU* 3.0 32.0 + - + +
43B VAL 3.8 3.1 - - - +
45B ALA* 1.3 73.0 - - - +
47B GLU* 1.3 61.8 + - - +
49B GLU* 4.6 0.2 - - - -
50B PHE* 2.9 59.6 + - + +
68B ALA* 4.6 11.9 - - + -
72B ILE* 5.1 2.2 - - + -
302B PM4 3.5 51.7 - - + +
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Residues in contact with GLU 47 (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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43B VAL* 3.0 37.2 + - - +
44B MET* 3.3 18.5 + - - +
46B LEU* 1.3 74.9 - - - +
48B GLU* 1.3 63.7 + - - +
51B ASP* 3.0 23.6 + - - -
52B THR 3.2 24.5 + - - +
53B GLU* 3.1 31.5 - - - +
54B ILE 2.9 29.2 + - - +
302B PM4 3.7 13.2 - - + -
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Residues in contact with GLU 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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1A SER* 3.0 25.2 + - - -
5A GLU* 3.2 32.7 - - - +
44B MET 3.0 16.8 + - - +
45B ALA* 3.6 6.7 - - - +
46B LEU 3.2 0.2 - - - -
47B GLU* 1.3 78.6 - - - +
49B GLU* 1.3 62.6 + - + +
51B ASP* 3.3 8.3 - - - +
410B ZN 4.0 0.9 - - - -
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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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1A SER* 3.2 41.7 + - - -
6A ARG* 3.8 10.4 + - - +
9A LYS* 4.2 15.1 + - - -
401A ZN 4.3 2.1 - - - -
6B ARG* 2.7 34.0 + - + +
10B ILE* 3.3 35.5 - - + +
45B ALA 3.1 11.4 + - - +
48B GLU* 1.3 79.7 - - + +
50B PHE* 1.3 81.6 + - + +
51B ASP* 4.5 0.2 - - - +
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Residues in contact with PHE 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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3B ILE* 4.0 21.3 - - + -
6B ARG* 4.1 31.0 - - + -
7B VAL* 3.8 27.4 - - + -
10B ILE* 4.0 2.9 - - + -
46B LEU* 2.9 33.7 + - + +
47B GLU 4.0 0.2 - - - -
49B GLU* 1.3 99.9 - - + +
51B ASP* 1.3 73.5 + - - +
52B THR* 3.3 8.0 + - + -
72B ILE* 3.5 38.4 - - + -
76B GLN* 3.7 22.7 - - + +
77B ALA 3.7 15.6 + - - -
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Residues in contact with ASP 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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1A SER 2.8 15.8 + - - -
401A ZN 2.2 27.4 - - - -
47B GLU 3.0 10.1 + - - -
48B GLU 3.3 0.9 - - - +
49B GLU 4.5 0.3 - - - +
50B PHE* 1.3 79.2 - - - +
52B THR* 1.3 58.8 + - - +
77B ALA* 3.6 33.1 - - + +
410B ZN 2.6 33.3 - - - -
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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