Contacts of the helix formed by residues 36 - 46 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A ASP 3.2 4.9 + - - -
35A GLU* 1.3 74.3 - - - +
37A VAL* 1.3 60.6 + - - +
38A GLY* 2.9 6.8 + - - -
39A SER* 2.6 31.1 + - - -
40A MET* 2.8 27.5 + - - +
80A PHE* 3.5 19.5 - - - -
108A LYS* 4.2 15.5 + - - +
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Residues in contact with VAL 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 GLU 3.6 1.2 + - - -
36A SER* 1.3 72.8 - - - +
38A GLY* 1.3 63.8 + - - +
40A MET* 3.7 7.5 - - - +
41A ALA* 3.3 3.6 + - - +
51A ASN* 3.0 24.2 + - - +
56A ARG* 3.2 43.1 - - - +
80A PHE* 3.8 20.6 - - + -
82A GLU* 5.2 0.7 - - - +
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Residues in contact with GLY 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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36A SER* 2.9 6.5 + - - -
37A VAL* 1.3 81.2 - - - +
39A SER* 1.3 58.5 + - - -
40A MET 3.0 1.3 - - - -
41A ALA* 2.8 29.6 + - - +
42A LYS* 3.6 5.9 + - - +
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Residues in contact with SER 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 GLU* 3.8 10.6 - - - +
36A SER* 2.6 39.0 + - - -
38A GLY* 1.3 73.6 - - - +
40A MET* 1.3 60.3 + - - +
42A LYS* 3.2 20.9 + - - +
43A ARG* 3.2 22.9 + - - +
108A LYS* 5.3 0.9 + - - -
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Residues in contact with MET 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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35A GLU* 3.4 23.8 - - + +
36A SER 2.8 19.1 + - - +
37A VAL 3.7 6.3 - - - +
39A SER* 1.3 76.8 + - - +
41A ALA* 1.3 64.3 + - - +
43A ARG* 3.5 35.0 - - + -
44A LEU* 3.0 40.0 + - + +
51A ASN* 3.9 2.2 - - - +
56A ARG* 3.5 37.0 - - + -
59A TYR* 4.6 21.5 - - + -
60A ARG* 3.5 20.6 - - - +
311A LEU* 4.9 1.6 - - + -
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Residues in contact with ALA 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 VAL 3.3 3.5 + - - +
38A GLY* 2.8 14.1 + - - +
40A MET* 1.3 80.7 - - - +
42A LYS* 1.3 58.9 + - + +
44A LEU* 3.8 1.2 - - - +
45A SER* 2.9 31.5 + - - -
51A ASN* 3.0 36.2 - - + +
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Residues in contact with LYS 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 GLY 3.6 6.2 + - - +
39A SER* 3.2 13.8 + - - +
41A ALA* 1.3 78.6 - - + +
43A ARG* 1.3 63.6 + - + +
45A SER* 2.8 24.8 + - - -
46A GLN* 3.3 15.6 - - - +
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Residues in contact with ARG 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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35A GLU* 2.6 41.5 + - - +
39A SER* 3.2 15.5 + - - +
40A MET* 3.5 26.9 - - + -
41A ALA 3.3 0.2 - - - -
42A LYS* 1.3 77.4 - - + +
44A LEU* 1.3 63.6 + - - +
46A GLN* 3.4 23.5 + - - +
47A ILE* 3.9 7.4 + - - +
303A GLY* 4.2 2.4 - - - -
304A ARG* 2.8 68.2 - - - +
307A GLN* 4.2 7.7 + - - +
311A LEU* 4.0 23.5 - - + +
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Residues in contact with LEU 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 MET* 3.0 26.4 + - + +
41A ALA* 3.9 3.8 - - - +
43A ARG* 1.3 73.2 - - - +
45A SER* 1.3 61.3 + - - +
47A ILE* 3.0 22.5 + - + +
48A GLY 2.4 21.8 - - - +
49A VAL* 3.6 37.7 - - + +
50A GLU 4.0 1.1 - - - +
51A ASN* 3.5 32.3 - - + +
55A ASN* 4.4 6.5 - - + +
56A ARG* 4.1 16.8 - - + -
59A TYR* 4.9 4.9 - - + -
311A LEU* 4.4 8.7 - - + -
314A TRP* 3.8 20.2 - - + -
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Residues in contact with SER 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 ALA 2.9 16.8 + - - -
42A LYS* 2.8 18.0 + - - -
44A LEU* 1.3 77.9 - - - +
46A GLN* 1.3 64.5 + - - +
47A ILE 3.0 0.2 - - - -
48A GLY* 3.0 20.0 + - - +
49A VAL 4.2 1.3 + - - -
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Residues in contact with GLN 46 (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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42A LYS* 3.3 14.3 + - - +
43A ARG* 3.6 16.2 + - - +
44A LEU 3.2 0.8 - - - -
45A SER* 1.3 83.8 + - - +
47A ILE* 1.3 63.5 + - + +
48A GLY 3.5 0.2 - - - -
304A ARG* 2.6 34.8 - - - +
315A ARG* 4.5 7.1 + - - -
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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