Contacts of the helix formed by residues 36 - 47 (chain A) in PDB entry 2FBH
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 ALA 36 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A GLN* 1.3 78.7 - - - +
37A ARG* 1.3 51.1 + - - +
38A TRP* 3.2 5.2 - - - +
39A LEU* 2.7 45.1 + - + +
40A VAL 3.5 2.4 + - - -
60A VAL* 4.8 10.5 - - + -
62A VAL* 5.4 5.4 - - + -
70A LEU* 3.8 25.0 - - + +
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Residues in contact with ARG 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A GLY 4.3 9.7 + - - -
33A LEU* 4.2 8.9 - - + +
34A SER* 2.7 24.8 + - - +
35A GLN* 2.8 24.0 + - - +
36A ALA* 1.3 75.9 - - - +
38A TRP* 1.3 62.6 + - - +
39A LEU 3.2 0.7 + - - -
40A VAL* 3.3 11.9 + - - +
41A LEU* 3.3 21.3 + - - +
69A ARG 4.6 4.0 + - - -
70A LEU* 3.5 41.2 + - + +
73A GLY* 3.1 28.0 - - - +
74A LEU* 3.9 18.3 - - + +
77A GLN* 3.7 29.3 + - - +
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Residues in contact with TRP 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ARG* 4.0 18.8 - - + -
24A LEU* 3.5 34.1 - - + -
25A ASP* 2.9 44.6 + - + +
28A LEU* 3.4 35.7 - - + -
33A LEU* 3.3 49.6 + - + +
35A GLN 4.2 8.4 + - - -
36A ALA* 2.9 2.6 + - - -
37A ARG* 1.3 78.9 - - - +
39A LEU* 1.3 101.8 + - + +
40A VAL 3.4 0.2 - - - -
41A LEU* 3.4 7.4 - - - +
42A LEU* 2.8 40.9 + - + +
107A ILE* 4.4 6.6 - - + +
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Residues in contact with LEU 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ARG* 4.4 15.3 - - - +
36A ALA* 2.7 26.5 + - + +
38A TRP* 1.3 105.3 - - + +
40A VAL* 1.3 57.3 + - - +
42A LEU* 4.2 9.0 - - + -
43A HIS* 2.8 70.2 + - + +
60A VAL* 3.5 35.4 - - + +
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Residues in contact with VAL 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A ALA 3.5 3.3 + - - +
37A ARG* 3.3 9.8 + - - +
39A LEU* 1.3 74.7 - - - +
41A LEU* 1.4 58.3 + - - +
43A HIS* 3.2 4.2 + - - +
44A LEU* 2.9 33.3 + - + +
56A LEU* 3.8 25.0 - - + +
60A VAL* 3.8 22.9 - - + -
67A LEU* 3.4 25.1 - - + -
70A LEU* 4.1 17.5 - - + -
71A LEU* 4.0 10.3 - - + -
74A LEU* 3.7 20.9 - - + -
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Residues in contact with LEU 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A LEU* 3.9 11.4 - - + -
37A ARG 3.3 9.5 + - - +
38A TRP* 3.4 8.7 - - - +
40A VAL* 1.4 72.8 - - - +
42A LEU* 1.3 67.9 + - - +
44A LEU* 3.2 6.2 + - + +
45A ALA* 2.9 23.9 + - - +
74A LEU* 4.0 29.6 - - + -
79A LEU* 4.2 9.2 - - + -
80A VAL* 4.2 8.7 - - + -
96A LEU* 3.8 24.5 - - + -
100A ALA* 5.1 1.3 - - + -
103A LEU* 3.4 32.5 - - + -
104A ILE* 3.6 17.2 - - + +
107A ILE* 3.8 14.6 - - + -
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Residues in contact with LEU 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ARG* 5.1 2.0 - - - +
24A LEU* 4.8 4.3 - - + -
38A TRP* 2.8 26.3 + - + +
39A LEU* 3.8 22.2 - - + +
40A VAL 3.2 0.4 - - - -
41A LEU* 1.3 76.1 - - - +
43A HIS* 1.3 65.2 + - + +
45A ALA* 3.1 7.4 + - + +
46A ARG* 3.1 60.2 + - - +
104A ILE* 5.2 1.1 - - + -
107A ILE* 3.7 21.1 - - + -
108A GLU* 3.0 42.6 - - + +
111A ALA* 4.4 11.0 - - + -
205A SO4 5.0 0.7 - - - +
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Residues in contact with HIS 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A LEU* 2.8 54.6 + - + +
40A VAL 3.7 3.4 - - - +
42A LEU* 1.3 79.1 - - + +
44A LEU* 1.3 63.3 + - - +
46A ARG* 3.2 13.7 + - - +
47A HIS* 3.0 26.7 + - - +
56A LEU* 4.2 6.1 - - + -
59A SER* 3.0 37.3 + - - +
60A VAL* 4.0 11.2 - - + -
204A ZN 2.8 27.4 - - - -
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Residues in contact with LEU 44 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A VAL* 2.9 28.1 + - + +
41A LEU* 3.6 8.1 - - - +
43A HIS* 1.3 77.3 - - - +
45A ALA* 1.3 63.8 + - - +
46A ARG 3.3 0.3 + - - -
47A HIS* 3.4 15.7 + - - +
49A ASP 5.3 1.4 - - - +
51A PRO* 3.6 39.3 - - + -
56A LEU* 4.2 7.4 - - + -
80A VAL* 3.6 31.0 - - + -
94A ILE* 3.7 25.8 - - + +
95A VAL* 5.3 0.2 - - - -
96A LEU* 3.9 28.0 - - + +
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Residues in contact with ALA 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A LEU 2.9 11.5 + - - +
42A LEU* 3.1 13.2 + - + +
44A LEU* 1.3 77.9 - - - +
46A ARG* 1.3 60.7 + - - +
47A HIS 3.9 3.1 + - - +
96A LEU* 3.9 9.8 - - - +
104A ILE* 3.2 35.2 - - + -
108A GLU* 4.4 9.8 - - + +
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Residues in contact with ARG 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ARG* 5.7 0.4 - - - +
42A LEU* 3.1 38.3 + - - +
43A HIS* 3.2 13.6 + - - +
44A LEU 3.1 0.6 - - - -
45A ALA* 1.3 79.3 - - - +
47A HIS* 1.3 78.3 + - + +
48A ARG 4.1 0.7 + - - -
108A GLU* 2.8 42.1 + - - +
111A ALA* 3.8 2.2 - - - +
115A ARG* 3.5 11.2 - - - +
205A SO4 2.9 42.6 + - - -
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Residues in contact with HIS 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A HIS 3.0 21.0 + - - +
44A LEU* 3.4 13.3 + - - +
45A ALA 3.5 3.0 - - - +
46A ARG* 1.3 89.5 + - + +
48A ARG* 1.3 64.3 + - - +
49A ASP* 3.7 15.7 - - + +
51A PRO* 6.0 2.5 - - + -
59A SER* 4.9 1.6 - - - -
204A ZN 2.0 37.7 - - - -
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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