Contacts of the helix formed by residues 35 - 44 (chain A) in PDB entry 1F0C
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 MET 35 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A ASP* 1.3 66.7 + - - +
37A ILE 3.5 2.0 - - - -
38A PHE* 3.2 22.2 + - + +
39A ARG* 2.9 30.1 + - - +
54A PRO* 4.9 6.5 - - + -
267A LEU* 2.9 51.3 + - + +
268A THR* 4.1 6.4 - - - +
269A ASP* 4.1 23.1 + - - +
272A PHE* 4.4 8.3 - - + -
373B VAL* 3.8 27.1 - - + -
382B ILE* 3.0 37.5 - - + -
385B VAL* 3.5 22.4 - - + -
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Residues in contact with ASP 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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35A MET* 1.3 73.7 - - - +
37A ILE* 1.3 66.1 + - + +
39A ARG* 3.3 26.6 + - - +
40A GLU* 3.3 20.3 + - - +
78A LYS* 5.1 9.9 + - - -
79A TYR* 3.0 31.1 + - + -
269A ASP* 5.0 3.2 + - - +
306A LEU* 3.5 20.5 - - - +
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Residues in contact with ILE 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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35A MET 3.5 0.6 - - - -
36A ASP* 1.3 75.9 - - + +
38A PHE* 1.3 67.6 + - - +
40A GLU* 3.3 1.8 + - - +
41A ILE* 3.0 43.6 + - + +
52A ILE* 4.1 11.0 - - + -
54A PRO* 5.7 6.7 - - + +
57A ILE* 3.5 38.4 - - + -
58A SER* 5.6 1.3 - - - +
61A LEU* 4.8 0.2 - - + -
79A TYR* 4.0 28.0 - - + -
299A LEU* 4.6 5.2 - - + -
302A ALA* 5.6 2.9 - - + -
303A LEU* 4.3 13.9 - - + -
306A LEU* 4.0 21.8 - - + -
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Residues in contact with PHE 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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35A MET* 3.2 22.2 + - + +
37A ILE* 1.3 77.7 - - - +
39A ARG* 1.3 62.8 + - + +
41A ILE* 3.3 2.0 + - - +
42A ALA* 2.8 38.5 + - + +
50A VAL* 3.7 28.3 - - + -
52A ILE* 3.7 19.9 - - + +
264A GLU* 4.4 19.1 - - + -
267A LEU* 3.8 28.7 - - + -
371B ILE* 4.5 6.7 - - + -
385B VAL* 3.9 21.3 - - + -
386B GLY* 3.8 23.6 - - - -
387B ARG* 3.7 25.6 - - + -
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Residues in contact with ARG 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 MET 2.9 12.8 + - - +
36A ASP* 3.3 45.4 + - - +
38A PHE* 1.3 79.7 - - + +
40A GLU* 1.3 65.3 + - - +
42A ALA* 3.6 3.8 - - - +
43A SER* 2.8 27.4 + - - -
264A GLU* 3.3 32.4 - - + +
265A GLN* 4.0 14.9 + - - -
267A LEU* 3.2 33.6 + - + +
268A THR* 4.2 12.8 + - - +
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Residues in contact with GLU 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 ASP 3.3 4.7 + - - +
37A ILE 3.3 6.5 + - - +
39A ARG* 1.3 77.4 - - - +
41A ILE* 1.3 65.3 + - - +
43A SER* 3.0 26.7 + - - -
44A SER* 3.0 13.2 + - - -
302A ALA* 3.8 18.7 - - + +
305A LYS* 3.6 36.2 + - - +
306A LEU* 3.1 43.4 - - + +
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Residues in contact with ILE 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 ILE* 3.0 27.8 + - + +
38A PHE 3.9 2.5 - - - +
40A GLU* 1.3 77.6 - - - +
42A ALA* 1.3 65.3 + - - +
44A SER* 3.1 18.6 + - - +
45A MET* 3.4 19.9 + - - +
50A VAL* 3.8 15.9 - - + -
52A ILE* 3.8 22.7 - - + -
297A TYR* 3.7 28.5 - - + -
298A ASN 6.0 0.9 - - - +
299A LEU* 3.5 30.1 - - + -
302A ALA* 4.2 17.9 - - + -
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Residues in contact with ALA 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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38A PHE* 2.8 36.3 + - + +
39A ARG* 3.6 4.3 - - - +
41A ILE* 1.3 72.7 - - - +
43A SER* 1.3 63.9 + - - +
45A MET 3.0 13.7 + - - -
46A LYS* 3.6 1.4 + - - -
50A VAL* 4.3 9.8 - - + +
264A GLU* 3.6 17.5 - - - +
387B ARG* 3.5 39.9 + - - +
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Residues in contact with SER 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 ARG 2.8 18.5 + - - -
40A GLU* 3.0 22.3 + - - -
42A ALA* 1.3 71.9 - - - +
44A SER* 1.3 60.8 + - - +
46A LYS* 3.3 34.0 - - - +
261A GLU* 6.0 1.8 - - - -
264A GLU* 4.3 6.4 + - - -
265A GLN* 6.2 4.5 - - - -
387B ARG* 5.3 0.2 - - - +
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Residues in contact with SER 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 GLU* 3.0 13.2 + - - -
41A ILE* 3.1 15.1 + - - +
42A ALA 3.1 0.4 + - - -
43A SER* 1.3 80.4 + - - +
45A MET* 1.3 64.7 + - - +
46A LYS* 3.7 2.0 - - - -
302A ALA* 5.5 3.6 - - - +
305A LYS* 4.5 18.8 - - - -
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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