Contacts of the helix formed by residues 36 - 46 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34D ASP 3.2 5.1 + - - -
35D GLU* 1.3 74.4 - - - +
37D VAL* 1.3 60.7 + - - +
38D GLY* 2.9 6.4 + - - -
39D SER* 2.6 32.0 + - - -
40D MET* 2.8 27.5 + - - +
80D PHE* 3.5 18.8 - - - -
108D LYS* 4.2 15.5 + - - +
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Residues in contact with VAL 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D GLU 3.6 1.2 + - - -
36D SER* 1.3 73.9 - - - +
38D GLY* 1.3 64.0 + - - +
40D MET* 3.7 7.0 - - - +
41D ALA 3.3 3.8 + - - -
51D ASN* 3.0 23.7 + - - +
56D ARG* 3.2 41.3 - - - +
80D PHE* 3.8 21.1 - - + -
82D GLU* 5.2 0.9 - - - +
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Residues in contact with GLY 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D SER* 2.9 6.4 + - - -
37D VAL* 1.3 81.6 - - - +
39D SER* 1.3 59.3 + - - -
40D MET 3.0 1.1 - - - -
41D ALA* 2.8 28.9 + - - +
42D LYS* 3.6 5.4 + - - +
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Residues in contact with SER 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D GLU* 3.8 10.3 - - - +
36D SER* 2.6 38.4 + - - -
38D GLY* 1.3 72.7 - - - +
40D MET* 1.3 60.4 + - - +
42D LYS* 3.2 21.5 + - - +
43D ARG* 3.2 23.4 + - - +
108D LYS* 5.3 0.9 + - - -
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Residues in contact with MET 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D GLU* 3.4 23.6 - - + +
36D SER 2.8 18.5 + - - +
37D VAL 3.7 6.3 - - - +
39D SER* 1.3 77.0 + - - +
41D ALA* 1.3 64.2 + - - +
43D ARG* 3.5 35.4 - - + -
44D LEU* 3.0 40.8 + - + +
51D ASN* 3.9 1.8 - - - +
56D ARG* 3.5 36.6 - - + -
59D TYR* 4.6 21.1 - - + -
60D ARG* 3.5 20.4 - - - +
311D LEU* 4.9 1.8 - - + -
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Residues in contact with ALA 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D VAL 3.3 3.7 + - - +
38D GLY* 2.8 13.5 + - - +
40D MET* 1.3 80.1 - - - +
42D LYS* 1.3 58.6 + - + +
44D LEU* 3.4 1.4 + - - +
45D SER* 2.9 31.4 + - - -
51D ASN* 3.0 35.7 - - + +
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Residues in contact with LYS 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D GLY 3.6 6.2 + - - +
39D SER* 3.2 14.1 + - - +
41D ALA* 1.3 78.3 - - + +
43D ARG* 1.3 63.2 + - + +
45D SER* 2.8 25.0 + - - -
46D GLN* 3.3 15.6 - - - +
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Residues in contact with ARG 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D GLU* 2.6 40.9 + - - +
39D SER* 3.2 15.8 + - - +
40D MET* 3.5 26.7 - - + -
42D LYS* 1.3 77.3 - - + +
44D LEU* 1.3 63.4 + - - +
46D GLN* 3.4 23.7 + - - +
47D ILE* 3.9 7.1 + - - +
303D GLY* 4.2 2.4 - - - -
304D ARG* 2.8 68.5 - - - +
307D GLN* 4.2 7.9 - - - +
311D LEU* 4.0 24.1 - - + +
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Residues in contact with LEU 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D MET* 3.0 26.2 + - + +
41D ALA* 3.9 3.8 - - - +
43D ARG* 1.3 74.3 - - - +
45D SER* 1.3 61.2 + - - +
47D ILE* 3.0 21.9 + - + +
48D GLY 2.4 21.7 - - - +
49D VAL* 3.6 37.2 - - + +
50D GLU 4.0 1.1 - - - +
51D ASN* 3.5 32.1 - - + +
55D ASN* 4.4 6.5 - - + -
56D ARG* 4.1 16.8 - - + -
59D TYR* 4.9 4.5 - - + -
311D LEU* 4.4 8.5 - - + -
314D TRP* 3.8 21.1 - - + -
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Residues in contact with SER 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D ALA 2.9 18.1 + - - -
42D LYS* 2.8 18.2 + - - -
43D ARG 3.3 0.2 - - - -
44D LEU* 1.3 76.8 - - - +
46D GLN* 1.3 64.3 + - - +
47D ILE 3.0 0.2 - - - -
48D GLY* 3.0 20.1 + - - +
49D VAL 4.2 1.5 + - - -
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Residues in contact with GLN 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D LYS* 3.3 13.5 + - - +
43D ARG* 3.6 15.3 + - - +
44D LEU 3.2 1.0 - - - -
45D SER* 1.3 84.3 + - - +
47D ILE* 1.3 62.8 + - + +
48D GLY 3.5 0.2 - - - -
304D ARG* 2.6 34.6 - - - +
315D ARG* 4.5 6.8 + - - -
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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