Contacts of the helix formed by residues 36 - 46 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34H ASP 3.2 4.9 + - - -
35H GLU* 1.3 74.1 - - - +
37H VAL* 1.3 60.6 + - - +
38H GLY* 2.9 5.9 + - - -
39H SER* 2.6 32.2 + - - -
40H MET* 2.8 27.4 + - - +
80H PHE* 3.5 19.1 - - - -
108H LYS* 4.2 15.9 + - - +
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Residues in contact with VAL 37 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35H GLU 3.6 0.8 + - - -
36H SER* 1.3 73.4 - - - +
38H GLY* 1.3 63.2 + - - +
40H MET* 3.7 7.7 - - - +
41H ALA 3.3 3.3 + - - -
51H ASN* 3.0 23.8 + - - +
56H ARG* 3.2 41.3 - - - +
80H PHE* 3.8 21.9 - - + -
82H GLU* 5.2 0.4 - - - +
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Residues in contact with GLY 38 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36H SER* 2.9 7.2 + - - -
37H VAL* 1.3 81.6 - - - +
39H SER* 1.3 59.3 + - - -
40H MET 3.0 1.1 - - - -
41H ALA* 2.8 29.6 + - - +
42H LYS* 3.6 5.6 + - - +
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Residues in contact with SER 39 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35H GLU* 3.8 10.8 - - - +
36H SER* 2.6 38.0 + - - -
38H GLY* 1.3 73.0 - - - +
40H MET* 1.3 60.8 + - - +
42H LYS* 3.2 20.8 + - - +
43H ARG* 3.2 22.1 + - - +
108H LYS* 5.3 1.2 + - - -
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Residues in contact with MET 40 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35H GLU* 3.4 22.4 - - + +
36H SER 2.8 18.1 + - - +
37H VAL 3.7 6.1 - - - +
39H SER* 1.3 76.3 + - - +
41H ALA* 1.3 64.0 + - - +
43H ARG* 3.4 36.0 + - + -
44H LEU* 3.0 40.1 + - + +
51H ASN* 3.9 2.5 - - - +
56H ARG* 3.5 37.7 - - + -
59H TYR* 4.6 21.3 - - + -
60H ARG* 3.5 21.1 - - - +
311H LEU* 4.9 1.6 - - + -
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Residues in contact with ALA 41 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37H VAL 3.3 3.1 + - - +
38H GLY* 2.8 13.3 + - - +
40H MET* 1.3 80.5 - - - +
42H LYS* 1.3 59.1 + - + +
44H LEU* 3.8 1.4 - - - +
45H SER* 2.9 30.9 + - - -
51H ASN* 3.0 35.1 - - + +
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Residues in contact with LYS 42 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38H GLY 3.6 6.3 + - - +
39H SER* 3.2 13.7 + - - +
41H ALA* 1.3 78.2 - - + +
43H ARG* 1.3 63.2 + - + +
45H SER* 2.8 24.4 + - - -
46H GLN* 3.3 15.0 - - - +
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Residues in contact with ARG 43 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35H GLU* 2.6 40.7 + - - +
39H SER* 3.2 16.5 + - - +
40H MET* 3.4 27.1 + - + -
42H LYS* 1.3 77.4 - - + +
44H LEU* 1.3 62.3 + - - +
46H GLN* 3.4 23.5 + - - +
47H ILE* 3.9 7.4 + - - +
303H GLY* 4.2 2.6 - - - -
304H ARG* 2.8 69.4 - - - +
307H GLN* 4.2 7.5 - - - +
311H LEU* 4.0 24.5 - - + +
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Residues in contact with LEU 44 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40H MET* 3.0 26.0 + - + +
41H ALA* 3.9 4.0 - - - +
43H ARG* 1.3 72.8 - - - +
45H SER* 1.3 61.5 + - - +
47H ILE* 3.0 22.8 + - + +
48H GLY 2.4 20.8 - - - +
49H VAL* 3.6 37.0 - - + +
50H GLU 4.0 1.1 - - - +
51H ASN* 3.5 32.8 - - - +
55H ASN* 4.4 6.3 - - + -
56H ARG* 4.1 16.8 - - + -
59H TYR* 4.9 4.9 - - + -
311H LEU* 4.4 8.1 - - + -
314H TRP* 3.8 21.5 - - + -
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Residues in contact with SER 45 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41H ALA 2.9 17.4 + - - -
42H LYS* 2.8 18.6 + - - -
44H LEU* 1.3 76.5 - - - +
46H GLN* 1.3 65.0 + - - +
47H ILE 3.0 0.2 - - - -
48H GLY* 3.0 20.2 + - - +
49H VAL 4.2 2.2 + - - -
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Residues in contact with GLN 46 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42H LYS* 3.3 13.0 + - - +
43H ARG* 3.6 15.7 + - - +
44H LEU 3.2 1.0 - - - -
45H SER* 1.3 83.4 + - - +
47H ILE* 1.3 63.9 + - + +
48H GLY 3.5 0.4 + - - -
304H ARG* 2.6 35.2 - - - +
315H 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