Contacts of the helix formed by residues 31 - 44 (chain B) in PDB entry 1XUQ
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 LYS 31 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177A ASN* 3.8 33.1 + - - +
26B ASN* 5.3 4.9 - - - -
27B ILE* 3.0 30.5 + - + +
30B THR* 1.3 97.3 - - - +
32B HIS* 1.3 65.6 + - - +
33B HIS 3.5 0.2 - - - -
34B ASN* 3.9 0.7 - - - +
35B THR* 2.9 32.5 + - - +
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Residues in contact with HIS 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A GLU* 3.8 8.3 - - - -
172A TYR* 2.7 33.8 + + - -
177A ASN* 3.6 23.1 - - + +
27B ILE* 3.0 27.7 + - + -
28B HIS* 3.4 24.2 - + + +
31B LYS* 1.3 77.0 - - - +
33B HIS* 1.3 63.9 + - - +
35B THR* 3.3 4.5 + - - -
36B TYR* 3.2 40.2 + - + -
83B HIS* 5.4 0.2 - - - +
169B HIS* 3.5 38.4 + + + +
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Residues in contact with HIS 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B LEU* 3.5 8.7 - - + +
7B PRO* 3.9 16.4 - - + -
28B HIS* 3.0 15.4 + - - +
29B HIS* 3.3 15.2 + - - +
31B LYS 3.5 0.2 - - - -
32B HIS* 1.3 72.0 - - - +
34B ASN* 1.3 63.5 + - - +
36B TYR* 3.1 18.5 + - - +
37B ILE* 3.1 15.2 + - + +
79B GLY 4.4 1.6 - - - -
80B HIS* 3.0 43.0 + - - -
83B HIS* 3.5 13.8 - - + +
84B THR* 3.4 27.4 + - - -
87B TRP* 2.9 29.7 + - + -
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Residues in contact with ASN 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B LEU* 4.0 28.4 - - + +
29B HIS 3.4 5.0 + - - +
30B THR* 3.4 29.5 - - - +
31B LYS 3.9 1.1 - - - +
32B HIS 3.4 0.2 - - - -
33B HIS* 1.3 78.6 - - - +
35B THR* 1.3 56.3 + - - +
37B ILE* 3.0 13.9 + - - +
38B THR* 2.8 38.9 + - - -
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Residues in contact with THR 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A ASN* 5.7 0.7 + - - -
31B LYS* 2.9 25.2 + - - +
32B HIS* 3.7 5.8 - - - -
33B HIS 3.2 0.2 - - - -
34B ASN* 1.3 73.0 - - - +
36B TYR* 1.3 68.9 + - + +
38B THR* 3.6 6.9 - - - -
39B ASN* 3.0 40.5 + - - +
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Residues in contact with TYR 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A PHE* 3.8 26.0 - + - -
32B HIS* 3.2 35.6 + - + -
33B HIS* 3.1 12.4 + - - +
35B THR* 1.3 77.7 - - + +
37B ILE* 1.3 57.7 + - - +
39B ASN 3.4 0.5 + - - -
40B LEU* 2.9 31.0 + - - +
75B ASN 4.2 3.6 - - - -
76B ASN* 3.5 36.4 - - - +
79B GLY* 3.8 18.6 - - - -
80B HIS* 4.1 7.0 - - - +
83B HIS* 3.5 24.0 - + - -
150B GLN* 2.8 24.5 + - + -
167B TRP* 3.6 18.7 - - - -
169B HIS* 4.2 6.6 - + - -
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Residues in contact with ILE 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B HIS* 3.3 32.3 - - + +
5B GLU* 3.5 8.5 - - - +
6B LEU* 3.4 49.4 - - + +
33B HIS* 3.1 10.2 + - + +
34B ASN* 3.0 14.0 + - - +
36B TYR* 1.3 73.7 - - - +
38B THR* 1.3 66.5 + - - +
40B LEU* 3.3 6.8 + - - +
41B ASN* 3.0 30.2 + - - +
80B HIS* 3.5 29.2 - - + +
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Residues in contact with THR 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B ASN* 2.8 28.4 + - - -
35B THR* 3.6 11.1 - - - -
37B ILE* 1.3 74.3 - - - +
39B ASN* 1.3 69.7 + - - +
41B ASN* 3.4 6.8 + - - +
42B ALA* 3.1 26.2 + - + +
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Residues in contact with ASN 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B THR* 3.0 32.5 + - - +
38B THR* 1.3 87.1 - - - +
40B LEU* 1.3 65.4 + - - +
42B ALA* 3.6 6.9 + - - +
43B ALA* 3.1 23.9 + - - +
72B ALA* 5.3 0.3 - - - +
76B ASN* 3.4 33.2 + - - +
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Residues in contact with LEU 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B HIS* 3.6 34.1 - - + +
36B TYR 2.9 19.2 + - - +
37B ILE* 3.6 4.9 - - - +
39B ASN* 1.3 76.3 - - - +
41B ASN* 1.3 63.6 + - - +
43B ALA* 3.1 5.5 + - + +
44B LEU* 3.0 38.8 + - + +
55B VAL* 4.1 9.9 - - + -
58B LEU* 4.0 17.3 - - + -
72B ALA 5.5 0.2 - - - -
73B VAL* 4.5 13.9 - - + -
76B ASN* 3.8 8.2 - - + +
77B GLY* 3.6 26.7 - - - +
80B HIS* 4.1 20.9 - - + -
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Residues in contact with ASN 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B LYS 3.5 12.0 + - - +
4B HIS* 3.1 56.6 + - - +
37B ILE* 3.0 26.2 + - - +
38B THR* 3.7 5.8 - - - +
40B LEU* 1.3 75.5 - - - +
42B ALA* 1.3 61.6 + - - +
44B LEU* 3.4 8.8 + - - +
45B GLU* 3.2 24.3 + - - +
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Residues in contact with ALA 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B THR* 3.1 18.1 + - + +
39B ASN* 3.8 9.4 - - - +
41B ASN* 1.3 75.9 - - - +
43B ALA* 1.3 61.5 + - - +
45B GLU* 3.1 41.6 + - - +
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Residues in contact with ALA 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B ASN 3.1 16.6 + - - +
40B LEU* 3.1 8.2 + - - +
42B ALA* 1.3 77.4 - - - +
44B LEU* 1.3 59.1 - - - +
45B GLU 3.6 2.3 + - - +
47B HIS* 3.8 4.9 - - - -
69B ILE* 3.5 37.1 - - + +
72B ALA* 3.7 31.6 - - + -
73B VAL* 4.8 5.4 - - + -
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Residues in contact with LEU 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B HIS* 3.8 33.7 - - + +
40B LEU* 3.0 31.2 + - + +
41B ASN* 3.6 8.1 - - - +
43B ALA* 1.3 75.9 - - - +
45B GLU* 1.3 62.6 + - - +
46B GLY 3.2 0.5 + - - -
47B HIS* 3.1 23.6 + - + -
48B ALA* 4.3 0.7 + - - -
50B LEU* 4.1 35.7 - - + -
51B ALA* 4.0 25.7 - - + +
58B LEU* 4.4 9.9 - - + -
69B ILE* 4.4 9.9 - - + -
73B VAL* 4.5 10.5 - - + -
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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