Contacts of the helix formed by residues 36 - 45 (chain C) in PDB entry 1FBA
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 GLY 36 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34C GLU 4.1 0.2 + - - -
35C SER* 1.3 70.6 - - - +
37C PRO* 1.3 70.2 - - - +
39C MET* 3.5 1.6 + - - +
40C GLY 3.0 9.7 + - - -
50C ASN* 2.9 26.2 + - - +
55C ARG* 3.9 29.3 - - - +
79C PHE* 4.4 11.2 - - - -
81C GLU* 5.4 1.1 + - - -
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Residues in contact with PRO 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C SER* 3.3 15.5 - - - +
36C GLY* 1.3 86.7 - - - +
38C THR* 1.3 64.3 + - - +
40C GLY* 3.1 10.9 + - - -
41C LYS* 3.3 16.0 + - - +
50C ASN* 4.4 4.7 - - - +
79C PHE* 6.2 0.2 - - + -
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Residues in contact with THR 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C GLU* 3.9 22.7 - - + -
35C SER* 3.0 24.1 + - - -
37C PRO* 1.3 74.8 - - - +
39C MET* 1.3 67.2 - - - +
41C LYS* 3.0 21.0 + - - +
42C ARG* 3.4 34.2 + - - +
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Residues in contact with MET 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C GLU* 4.0 20.4 - - + +
35C SER 2.7 20.6 + - - +
36C GLY 3.8 3.6 - - - +
38C THR* 1.3 74.6 - - - +
40C GLY* 1.3 57.4 + - - +
42C ARG* 3.2 19.7 + - + +
43C LEU* 3.0 62.7 + - + +
55C ARG* 3.9 26.0 - - + -
58C TYR* 3.3 32.3 - - + -
59C ARG* 3.6 31.0 - - - +
306C GLN* 5.1 0.4 - - - +
310C LEU* 4.3 4.9 - - + -
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Residues in contact with GLY 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C GLY 3.0 8.1 + - - -
37C PRO 3.4 4.9 - - - -
38C THR 3.0 1.4 - - - -
39C MET* 1.3 76.9 - - - +
41C LYS* 1.3 56.5 + - - +
43C LEU* 3.4 2.5 + - - +
44C GLN* 2.9 33.0 + - - +
50C ASN* 3.3 38.9 - - - +
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Residues in contact with LYS 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C PRO 3.3 10.8 + - - +
38C THR* 3.0 12.1 + - - +
40C GLY* 1.3 74.2 - - - +
42C ARG* 1.3 81.1 + - - +
44C GLN* 3.4 13.2 + - - +
45C ASP* 3.2 25.7 + - - +
358C VAL* 5.6 9.4 - - + +
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Residues in contact with ARG 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C GLU* 4.9 12.9 + - + +
38C THR* 3.7 37.4 + - + +
39C MET* 3.2 20.5 + - + +
41C LYS* 1.3 90.0 - - - +
43C LEU* 1.3 63.7 + - - +
45C ASP* 3.3 28.9 + - - +
46C ILE* 3.4 11.6 - - - +
303C ARG* 3.5 59.0 - - - +
310C LEU* 3.8 25.3 - - + +
358C VAL* 4.9 11.5 - - - +
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Residues in contact with LEU 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C MET* 3.0 51.0 + - + +
40C GLY* 3.8 4.7 - - - +
42C ARG* 1.3 74.5 - - - +
44C GLN* 1.3 61.4 + - - +
46C ILE* 2.9 10.1 + - + +
47C GLY 2.9 5.5 + - - -
48C VAL* 2.7 44.0 + - + +
49C GLU 4.4 13.9 - - - +
50C ASN* 4.3 8.1 - - - +
54C ASN* 4.5 10.1 - - + -
55C ARG* 4.2 20.2 - - + +
58C TYR* 4.6 1.8 - - + -
310C LEU* 3.8 17.0 - - + -
313C TRP* 4.1 18.4 - - + -
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Residues in contact with GLN 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C GLY 2.9 19.2 + - - +
41C LYS* 3.6 15.3 - - - +
42C ARG 3.4 0.2 - - - -
43C LEU* 1.3 77.7 - - - +
45C ASP* 1.3 56.3 + - - +
47C GLY* 2.8 21.1 + - - -
48C VAL 3.4 10.0 + - - +
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Residues in contact with ASP 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C LYS 3.2 13.9 + - - +
42C ARG* 3.3 28.0 - - - +
43C LEU 3.1 0.8 - - - -
44C GLN* 1.3 79.3 - - + +
46C ILE* 1.3 68.6 + - - +
47C GLY 3.2 0.9 - - - -
303C ARG* 5.3 3.5 + - - -
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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