Contacts of the helix formed by residues 36 - 46 (chain C) in PDB entry 1XFB
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 SER 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 ASP 3.2 5.1 + - - -
35C GLU* 1.3 73.7 - - - +
37C VAL* 1.3 61.1 + - - +
38C GLY* 2.9 5.8 + - - -
39C SER* 2.6 31.6 + - - -
40C MET* 2.8 27.2 + - - +
80C PHE* 3.5 20.6 - - - -
108C LYS* 4.2 15.1 + - - +
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Residues in contact with VAL 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 GLU 3.6 0.8 + - - -
36C SER* 1.3 73.2 - - - +
38C GLY* 1.3 61.8 + - - +
40C MET* 3.7 7.2 - - - +
41C ALA 3.3 3.3 + - - -
51C ASN* 3.0 24.8 + - - +
56C ARG* 3.2 42.2 - - - +
80C PHE* 3.8 21.7 - - + -
82C GLU* 5.2 0.7 - - - +
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Residues in contact with GLY 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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36C SER* 2.9 6.8 + - - -
37C VAL* 1.3 81.8 - - - +
39C SER* 1.3 59.5 + - - -
40C MET 3.0 1.1 - - - -
41C ALA* 2.8 28.9 + - - +
42C LYS* 3.6 5.6 + - - +
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Residues in contact with SER 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C GLU* 3.8 10.6 - - - +
36C SER* 2.6 38.9 + - - -
38C GLY* 1.3 73.2 - - - +
40C MET* 1.3 61.6 + - - +
42C LYS* 3.2 20.3 + - - +
43C ARG* 3.2 22.0 + - - +
108C LYS* 5.3 0.9 + - - -
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Residues in contact with MET 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C GLU* 3.4 24.2 - - + +
36C SER 2.8 18.7 + - - +
37C VAL 3.7 6.5 - - - +
39C SER* 1.3 77.4 + - - +
41C ALA* 1.3 63.5 + - - +
43C ARG* 3.4 35.6 + - + -
44C LEU* 3.0 41.2 + - + +
51C ASN* 3.9 2.2 - - - +
56C ARG* 3.5 36.3 - - + -
59C TYR* 4.6 20.6 - - + -
60C ARG* 3.5 20.4 - - - +
307C GLN* 5.6 0.2 - - - +
311C LEU* 4.9 1.8 - - + -
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Residues in contact with ALA 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 VAL 3.3 3.0 + - - +
38C GLY* 2.8 14.1 + - - +
40C MET* 1.3 80.1 - - - +
42C LYS* 1.3 58.9 + - + +
44C LEU* 3.8 1.4 - - - +
45C SER* 2.9 31.3 + - - -
51C ASN* 3.0 36.0 - - + +
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Residues in contact with LYS 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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38C GLY 3.6 5.8 + - - +
39C SER* 3.2 14.6 + - - +
41C ALA* 1.3 79.1 - - + +
43C ARG* 1.3 63.1 + - + +
45C SER* 2.8 24.8 + - - -
46C GLN* 3.3 16.1 - - - +
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Residues in contact with ARG 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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35C GLU* 2.6 42.5 + - - +
39C SER* 3.2 16.2 + - - +
40C MET* 3.5 27.1 - - + -
41C ALA 3.3 0.2 - - - -
42C LYS* 1.3 77.9 - - + +
44C LEU* 1.3 65.4 + - - +
46C GLN* 3.4 24.1 + - - +
47C ILE* 3.9 7.1 + - - +
303C GLY* 4.2 2.2 - - - -
304C ARG* 2.8 69.5 - - - +
307C GLN* 4.2 7.7 - - - +
311C LEU* 4.0 23.0 - - + +
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Residues in contact with LEU 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 MET* 3.0 25.8 + - + +
41C ALA* 3.9 3.4 - - - +
43C ARG* 1.3 74.0 - - - +
45C SER* 1.3 61.6 + - - +
47C ILE* 3.0 23.1 + - + +
48C GLY 2.4 21.9 - - - +
49C VAL* 3.6 36.8 - - + +
50C GLU 4.0 0.9 - - - +
51C ASN* 3.5 32.8 - - + +
55C ASN* 4.4 6.1 - - + -
56C ARG* 4.1 17.3 - - + -
59C TYR* 4.9 5.2 - - + -
311C LEU* 4.4 8.7 - - + -
314C TRP* 3.8 20.2 - - + -
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Residues in contact with SER 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 ALA 2.9 17.6 + - - -
42C LYS* 2.8 18.1 + - - -
44C LEU* 1.3 76.9 - - - +
46C GLN* 1.3 63.9 + - - +
48C GLY* 3.0 20.5 + - - +
49C VAL 4.2 1.5 + - - -
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Residues in contact with GLN 46 (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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42C LYS* 3.3 13.4 + - - +
43C ARG* 3.6 15.8 + - - +
44C LEU 3.2 0.8 - - - -
45C SER* 1.3 83.2 + - - +
47C ILE* 1.3 63.3 + - + +
48C GLY 3.5 0.2 - - - -
304C ARG* 2.6 34.6 + - - +
315C ARG* 4.5 6.9 + - - -
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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