Contacts of the helix formed by residues 30 - 51 (chain B) in PDB entry 1XR2
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 THR 30 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24B PHE* 3.9 2.9 - - - -
29B ILE* 1.3 77.7 - - - +
31B GLU* 1.3 59.4 + - - +
32B GLU* 3.4 10.1 + - - +
33B GLN* 2.8 41.9 + - - +
34B PHE* 2.8 27.7 + - - +
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Residues in contact with GLU 31 (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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24B PHE* 3.5 26.3 - - + -
30B THR* 1.3 72.2 - - - +
32B GLU* 1.3 61.5 + - - +
34B PHE* 3.1 4.9 + - - +
35B GLU* 2.9 33.6 + - + +
87B LEU* 4.6 11.2 - - + +
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Residues in contact with GLU 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B THR* 3.2 9.3 + - - +
31B GLU* 1.3 79.8 - - - +
33B GLN* 1.3 61.5 + - + +
35B GLU* 3.7 6.9 + - - +
36B GLU* 3.2 20.8 + - - +
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Residues in contact with GLN 33 (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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28B LYS 4.6 1.4 + - - +
29B ILE* 3.4 19.3 - - + +
30B THR* 2.8 46.5 + - - +
31B GLU 3.1 0.4 - - - -
32B GLU* 1.3 77.4 - - + +
34B PHE* 1.3 66.4 + - - +
35B GLU 3.2 0.2 - - - -
36B GLU* 3.1 16.2 + - - +
37B GLU* 3.1 14.2 + - - +
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Residues in contact with PHE 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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20B ALA* 3.7 23.1 - - + -
21B LEU* 3.5 41.5 - - + -
24B PHE* 3.9 22.7 - + + -
29B ILE* 5.0 2.6 - - - +
30B THR 2.8 14.3 + - - +
31B GLU* 3.4 7.6 - - - +
33B GLN* 1.3 78.3 - - - +
35B GLU* 1.3 65.3 + - + +
37B GLU* 3.4 6.8 + - - +
38B MET* 3.1 53.3 + - + +
63B TYR* 3.6 35.0 - + + -
87B LEU* 3.9 26.5 - - + -
91B PHE* 4.2 4.3 - + - -
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Residues in contact with GLU 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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31B GLU 2.9 18.1 + - - +
32B GLU* 3.9 6.3 - - - +
34B PHE* 1.3 80.7 - - + +
36B GLU* 1.3 59.6 + - - +
38B MET* 3.1 5.4 + - - +
39B ASN* 2.8 52.2 + - - +
42B ARG* 4.0 2.3 + - - -
63B TYR* 2.7 38.4 + - - -
87B LEU* 5.5 5.8 - - + +
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Residues in contact with GLU 36 (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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32B GLU 3.2 13.7 + - - +
33B GLN* 3.1 12.4 + - - +
35B GLU* 1.3 78.5 - - - +
37B GLU* 1.3 63.0 + - - +
39B ASN* 3.4 9.5 + - - +
40B LYS* 3.2 29.8 + - + +
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Residues in contact with GLU 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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16B GLU* 5.4 5.3 - - + +
20B ALA* 4.0 23.6 - - + -
33B GLN 3.1 11.0 + - - +
34B PHE 3.6 8.5 - - - +
36B GLU* 1.3 73.5 - - - +
38B MET* 1.3 68.3 + - + +
40B LYS* 3.1 21.7 + - - +
41B LEU* 3.0 24.8 + - + +
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Residues in contact with MET 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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17B PHE* 3.9 26.2 - - + +
20B ALA* 3.7 29.8 - - + -
34B PHE* 3.1 32.6 + - + +
35B GLU* 3.4 7.4 - - - +
37B GLU* 1.3 77.4 - - - +
39B ASN* 1.3 63.3 + - - +
41B LEU* 2.9 19.1 + - + -
42B ARG* 2.9 34.9 + - - +
61B LEU* 3.1 16.9 - - + +
63B TYR* 3.4 38.6 - - + +
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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 GLU* 2.8 35.8 + - - +
36B GLU* 3.7 8.7 - - - +
38B MET* 1.3 72.2 - - - +
40B LYS* 1.3 63.7 + - + +
42B ARG* 2.9 28.8 + - - +
43B MET* 3.1 26.6 + - + +
135B PHE* 3.6 35.3 - - + -
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Residues in contact with LYS 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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16B GLU* 6.6 0.2 - - - -
36B GLU* 3.2 13.7 + - + +
37B GLU* 3.1 24.3 + - - +
39B ASN* 1.3 75.8 - - + +
41B LEU* 1.3 59.6 + - + +
43B MET* 3.3 8.5 + - - +
44B TYR* 2.9 28.7 + - - +
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Residues in contact with LEU 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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10B LYS 3.7 25.1 - - - +
11B ILE 4.5 0.2 - - - +
12B GLY* 4.0 14.1 - - - -
16B GLU* 4.0 28.7 - - + +
17B PHE* 3.8 30.1 - - + +
37B GLU* 3.0 12.4 + - + +
38B MET* 2.9 29.9 + - + +
40B LYS* 1.3 75.2 - - + +
42B ARG* 1.3 64.9 + - - +
44B TYR* 3.2 12.1 + - + +
45B MET* 2.9 31.2 + - + +
61B LEU* 3.9 9.2 - - + -
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Residues in contact with ARG 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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35B GLU* 4.0 3.6 + - - -
38B MET* 2.9 13.5 + - - +
39B ASN* 2.9 41.3 + - - +
41B LEU* 1.3 78.2 - - - +
43B MET* 1.3 57.1 + - - +
45B MET* 3.3 8.2 + - - +
46B VAL* 3.0 32.4 + - - +
61B LEU* 3.5 28.7 + - + +
63B TYR* 2.8 36.2 + - - -
128B LYS* 6.3 0.8 - - - +
132B ASP* 3.0 29.8 + - - +
135B PHE* 3.7 22.8 - - + -
136B PHE* 3.6 17.9 - - + -
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Residues in contact with MET 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 17.2 + - - +
40B LYS* 3.6 10.3 - - - +
42B ARG* 1.3 74.9 - - - +
44B TYR* 1.3 65.3 + - - +
46B VAL* 3.2 13.1 - - + +
47B GLU* 2.9 27.6 + - - +
135B PHE* 4.4 13.0 - - + -
136B PHE* 4.2 16.6 - - - -
139B LYS* 4.3 16.2 - - + +
141B ILE* 4.1 20.4 - - + -
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Residues in contact with TYR 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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8B PHE* 4.0 13.3 - + - -
9B PRO 5.2 0.9 - - - -
10B LYS 5.9 0.2 - - - -
12B GLY* 4.2 24.9 - - - -
13B GLU* 2.5 46.4 + - + +
16B GLU* 5.5 4.0 - - - +
40B LYS 2.9 14.1 + - - +
41B LEU* 3.4 17.9 - - + +
43B MET* 1.3 76.9 - - - +
45B MET* 1.3 70.6 + - + +
47B GLU* 3.9 5.0 - - - +
48B ASN* 2.9 50.4 + - - -
316B VAL* 3.3 11.7 - - + +
336B LYS* 4.4 2.8 - - - -
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Residues in contact with MET 45 (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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8B PHE* 3.3 34.3 - - + +
9B PRO 3.9 14.1 - - - +
10B LYS* 4.0 26.5 - - + +
41B LEU* 2.9 23.1 + - + +
42B ARG* 3.5 6.3 - - - +
44B TYR* 1.3 83.7 - - + +
46B VAL* 1.3 64.2 + - + +
48B ASN* 3.1 9.2 + - - +
49B TYR* 3.1 32.2 + - + -
60B GLU* 4.0 33.0 - - + +
61B LEU* 4.4 18.8 - - - +
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Residues in contact with VAL 46 (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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42B ARG 3.0 12.3 + - - +
43B MET* 3.2 29.6 - - + +
45B MET* 1.3 76.5 - - + +
47B GLU* 1.3 59.6 + - - +
49B TYR* 3.7 10.0 - - + +
50B ARG* 3.0 27.9 + - - +
56B ILE* 3.7 25.8 - - + +
57B PRO 4.1 9.6 - - - +
136B PHE* 3.4 38.8 - - + -
141B ILE* 4.2 16.4 - - + -
143B THR* 4.8 0.2 - - + -
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Residues in contact with GLU 47 (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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43B MET 2.9 19.4 + - - +
44B TYR* 3.9 5.8 - - - +
46B VAL* 1.3 78.6 - - + +
48B ASN* 1.3 66.6 + - - +
50B ARG* 3.4 12.5 + - - +
51B LYS* 3.2 54.8 + - - +
141B ILE* 5.7 4.7 - - - +
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Residues in contact with ASN 48 (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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8B PHE* 3.7 19.7 - - + -
44B TYR* 2.9 57.8 + - - -
45B MET 3.1 9.1 + - - +
47B GLU* 1.3 79.6 - - - +
49B TYR* 1.3 61.0 - - - +
51B LYS* 3.6 8.7 + - - +
52B ASN* 3.1 27.3 + - - +
336B LYS* 3.8 28.6 - - - +
339B LEU* 3.7 15.4 - - + +
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Residues in contact with TYR 49 (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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5B ALA* 3.7 39.0 - - + -
6B PHE* 3.5 1.4 - - - -
7B GLY 3.3 6.8 + - - -
8B PHE* 2.9 40.7 + - + +
45B MET* 3.1 35.2 + - + -
46B VAL* 3.7 11.4 - - + +
47B GLU 3.2 0.2 - - - -
48B ASN* 1.3 73.8 - - - +
50B ARG* 1.3 56.1 + - - +
52B ASN* 2.8 23.6 + - - -
53B VAL* 2.8 24.7 + - + +
56B ILE* 4.4 12.1 - - + -
57B PRO* 3.8 24.7 - - + -
60B GLU* 2.7 29.2 + - - -
311B LEU* 5.5 0.2 - - + -
339B LEU* 4.2 11.7 - - + -
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Residues in contact with ARG 50 (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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46B VAL 3.0 18.9 + - - +
47B GLU* 3.8 17.7 - - - +
49B TYR* 1.3 74.7 - - - +
51B LYS* 1.3 62.5 + - - +
52B ASN* 3.0 2.1 + - - -
53B VAL 3.6 13.9 + - - +
56B ILE* 4.2 19.7 - - + +
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Residues in contact with LYS 51 (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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47B GLU* 3.2 42.9 + - + +
48B ASN* 3.8 9.9 - - - +
49B TYR 3.2 0.2 - - - -
50B ARG* 1.3 78.3 - - - +
52B ASN* 1.3 68.3 + - - +
343B LYS* 3.5 22.0 - - - +
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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
------------------------------------------------------------
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