Contacts of the helix formed by residues 33 - 47 (chain A) in PDB entry 2FBI
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 THR 33 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A LEU* 4.8 1.1 - - - -
32A LEU* 1.3 76.3 - - - +
34A GLU* 1.3 63.3 + - - +
35A GLN* 3.3 19.9 + - - +
36A GLN* 2.9 40.5 + - - +
37A TRP* 3.1 20.3 + - - +
68A VAL* 5.7 0.7 - - - +
71A ARG* 5.0 7.9 - - - +
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Residues in contact with GLU 34 (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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16A ARG* 3.2 20.4 + - - +
20A MET* 3.7 19.3 - - + -
24A ARG* 2.6 52.7 + - - +
27A LEU* 4.1 12.8 - - + +
32A LEU 4.0 1.0 + - - -
33A THR* 1.3 72.7 - - - +
35A GLN* 1.3 78.9 + - - +
37A TRP* 3.6 4.1 - - + +
38A ARG* 2.8 46.6 + - + +
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Residues in contact with GLN 35 (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 THR* 3.1 22.7 + - - +
34A GLU* 1.3 98.2 + - - +
36A GLN* 1.3 65.7 + - - +
38A ARG* 3.6 25.6 + - - +
39A VAL* 3.3 27.9 + - - +
60A ILE* 3.4 20.5 - - + +
68A VAL* 4.3 15.5 - - + -
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Residues in contact with GLN 36 (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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31A GLY 4.5 1.9 - - - +
32A LEU* 3.2 17.3 - - + +
33A THR* 2.9 42.5 + - - +
35A GLN* 1.3 77.5 - - - +
37A TRP* 1.3 55.8 + - - +
39A VAL* 3.3 4.4 + - - +
40A ILE* 2.9 34.4 + - + +
68A VAL* 4.2 17.2 - - + +
71A ARG* 3.2 48.6 + - - +
72A LEU* 3.8 31.5 - - + +
75A ASP* 5.0 1.4 + - - -
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Residues in contact with TRP 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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23A PHE* 6.2 0.9 - - + -
27A LEU* 3.6 28.7 - - + -
32A LEU* 4.7 4.9 - - + +
33A THR 3.1 14.7 + - - +
34A GLU* 3.3 10.7 + - + +
36A GLN* 1.3 72.5 - - - +
38A ARG* 1.4 57.7 + - + +
40A ILE* 3.6 29.6 - - + +
41A ARG* 2.7 73.1 + - + +
101A CYS* 5.1 2.0 - - - -
102A PHE* 3.5 32.5 - + - -
105A MET* 3.7 37.2 - - + -
106A SER* 5.5 1.1 - - - -
109A MET* 4.0 31.2 - - + +
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Residues in contact with ARG 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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16A ARG* 3.2 33.8 - - - +
34A GLU* 2.8 43.8 + - + +
35A GLN* 3.8 21.5 - - - +
36A GLN 3.3 0.2 - - - -
37A TRP* 1.4 72.4 - - + +
39A VAL* 1.3 60.1 + - - +
41A ARG* 3.5 6.9 + - - +
42A ILE* 3.0 37.7 + - + +
58A ALA* 2.9 30.6 + - + +
59A CYS* 2.8 27.5 + - - +
60A ILE* 3.6 12.9 - - - +
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Residues in contact with VAL 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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35A GLN 3.3 14.2 + - - +
36A GLN 3.5 8.5 - - - +
38A ARG* 1.3 74.9 - - - +
40A ILE* 1.3 66.2 + - - +
42A ILE* 3.2 1.9 + - - +
43A LEU* 2.9 46.0 + - + +
54A LEU* 4.2 8.1 - - + -
58A ALA* 4.1 10.8 - - + -
60A ILE* 3.4 20.6 - - + -
65A MET* 4.0 17.7 - - + -
68A VAL* 4.0 5.6 - - + -
69A LEU* 4.1 12.3 - - + -
72A LEU* 3.9 21.8 - - + -
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Residues in contact with ILE 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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32A LEU* 3.9 28.7 - - + -
36A GLN 2.9 25.1 + - - +
37A TRP* 3.3 29.1 + - + +
39A VAL* 1.3 75.7 - - + +
41A ARG* 1.3 58.1 + - - +
44A ARG* 2.8 32.1 + - - +
72A LEU* 4.3 11.0 - - + -
77A ILE* 4.0 28.9 - - + -
94A LEU* 3.8 20.5 - - + +
98A GLY 4.7 2.5 - - - +
101A CYS* 4.7 5.8 - - - -
102A PHE* 4.1 22.4 - - + +
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Residues in contact with ARG 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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37A TRP* 2.7 57.3 + - + +
38A ARG* 3.6 7.9 - - - +
40A ILE* 1.3 74.4 - - - +
42A ILE* 1.3 59.2 + - + +
44A ARG* 3.6 5.4 - - - +
45A GLN* 3.1 33.6 + - - +
102A PHE* 3.8 30.9 - - - -
109A MET* 6.6 0.2 - - - -
113A TYR* 4.4 25.5 + - - -
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Residues in contact with ILE 42 (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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38A ARG* 3.0 24.7 + - + +
39A VAL 3.2 2.9 + - - +
41A ARG* 1.3 75.3 - - + +
43A LEU* 1.3 63.6 + - - +
45A GLN* 4.6 2.7 - - - +
46A GLN* 2.8 45.4 + - - +
49A MET* 3.8 25.1 - - + -
54A LEU* 3.8 18.2 - - + -
57A GLN* 3.6 12.3 - - + +
58A ALA* 2.9 48.0 - - + +
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Residues in contact with LEU 43 (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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39A VAL* 2.9 29.2 + - + +
40A ILE 3.9 0.2 - - - +
42A ILE* 1.3 78.6 - - - +
44A ARG* 1.3 57.0 + - - +
47A GLY* 2.9 40.0 + - - +
49A MET* 3.9 15.7 - - + -
54A LEU* 3.9 18.2 - - + -
78A VAL* 3.8 20.6 - - + -
92A VAL* 3.4 46.2 - - + +
93A ASN* 4.3 7.4 - - - -
94A LEU* 3.8 23.5 + - + +
99A GLN* 5.0 2.9 + - - -
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Residues in contact with ARG 44 (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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40A ILE 2.8 18.8 + - - +
41A ARG* 3.6 4.9 - - - +
43A LEU* 1.3 78.9 - - - +
45A GLN* 1.3 66.1 + - + +
47A GLY* 3.9 3.5 + - - -
94A LEU* 3.5 9.8 - - + +
99A GLN* 2.9 49.2 + - - +
102A PHE* 3.3 52.7 - - + -
103A VAL* 3.9 15.0 - - - +
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Residues in contact with GLN 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 ARG* 3.1 18.3 + - - +
42A ILE* 4.3 2.5 - - - +
44A ARG* 1.3 83.3 - - + +
46A GLN* 1.3 69.4 - - + +
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Residues in contact with GLN 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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42A ILE* 2.8 31.3 + - + +
45A GLN* 1.3 85.0 - - + +
47A GLY* 1.3 61.9 + - - +
48A GLU 4.2 4.2 + - - +
49A MET* 3.4 21.4 - - + +
53A GLN* 5.6 0.2 + - - -
57A GLN* 2.8 40.8 + - - -
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Residues in contact with GLY 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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42A ILE 4.5 0.3 - - - +
43A LEU* 2.9 36.6 + - - +
44A ARG 3.9 2.8 + - - -
45A GLN 3.6 2.0 - - - -
46A GLN* 1.3 78.5 - - - +
48A GLU* 1.3 69.4 + - - +
49A MET* 3.6 4.7 + - - +
93A ASN* 5.1 2.0 - - - -
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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