Contacts of the helix formed by residues 30 - 51 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A PHE* 4.1 1.3 - - - -
29A ILE* 1.3 78.5 - - - +
31A GLU* 1.3 59.0 + - - +
32A GLU* 3.0 11.3 + - - +
33A GLN* 2.6 50.5 + - + +
34A PHE* 2.9 27.0 + - - +
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Residues in contact with GLU 31 (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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24A PHE* 3.5 29.8 - - + -
30A THR* 1.3 74.3 - - - +
32A GLU* 1.3 57.7 + - - +
34A PHE* 3.3 2.5 + - + +
35A GLU* 3.0 30.8 + - + +
87A LEU* 3.2 45.5 + - + +
88A SER 5.6 0.7 + - - -
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Residues in contact with GLU 32 (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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30A THR* 3.0 8.4 + - - +
31A GLU* 1.3 78.6 - - - +
33A GLN* 1.3 62.5 + - - +
35A GLU* 3.1 8.8 + - + +
36A GLU* 2.8 51.4 + - + +
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Residues in contact with GLN 33 (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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28A LYS 4.5 1.2 - - - +
29A ILE* 3.2 25.3 - - + +
30A THR* 2.6 54.9 + - + +
32A GLU* 1.3 78.1 - - + +
34A PHE* 1.3 57.2 + - - +
36A GLU* 3.3 19.3 + - - +
37A GLU* 2.9 29.6 + - - +
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Residues in contact with PHE 34 (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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20A ALA* 3.3 38.4 - - + -
21A LEU* 3.7 26.9 - - + -
24A PHE* 3.8 17.7 - + + -
29A ILE* 4.0 8.0 - - + +
30A THR 2.9 13.9 + - - +
31A GLU* 3.3 12.6 - - - +
33A GLN* 1.3 76.5 - - - +
35A GLU* 1.3 60.2 + - - +
37A GLU* 3.1 5.9 + - - +
38A MET* 2.9 66.3 + - + +
63A TYR* 3.9 24.2 - + + -
87A LEU* 4.0 22.0 - - + -
91A PHE* 4.3 7.9 - + - -
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Residues in contact with GLU 35 (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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31A GLU* 3.0 20.9 + - + +
32A GLU* 3.1 12.8 + - + +
34A PHE* 1.3 80.7 - - + +
36A GLU* 1.3 58.0 + - + +
38A MET* 3.1 6.4 + - - +
39A ASN* 2.8 47.6 + - - +
42A ARG* 4.3 1.0 + - - -
63A TYR* 2.8 41.9 + - - -
87A LEU* 5.0 3.3 - - + +
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Residues in contact with GLU 36 (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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32A GLU* 2.8 37.2 + - + +
33A GLN* 3.5 23.1 - - - +
35A GLU* 1.3 75.8 - - + +
37A GLU* 1.3 63.2 + - - +
39A ASN* 3.2 11.4 + - - +
40A LYS* 3.1 33.7 + - - +
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Residues in contact with GLU 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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16A GLU* 3.6 21.1 - - - +
20A ALA* 3.4 31.4 - - + -
29A ILE* 5.5 2.2 - - + -
33A GLN 2.9 14.2 + - - +
34A PHE* 3.1 9.4 + - - +
36A GLU* 1.3 75.6 - - - +
38A MET* 1.3 63.5 + - + +
40A LYS* 3.2 25.5 + - - +
41A LEU* 2.9 53.3 - - + +
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Residues in contact with MET 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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17A PHE* 3.9 21.5 - - + +
20A ALA* 3.6 31.0 - - + -
34A PHE* 2.9 40.1 + - + +
35A GLU 3.1 7.4 + - - +
37A GLU* 1.3 77.7 - - + +
39A ASN* 1.3 58.3 + - - +
41A LEU* 3.2 12.7 + - + -
42A ARG* 3.0 27.4 + - - +
61A LEU* 3.1 29.9 - - + +
63A TYR* 3.4 47.6 - - + +
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Residues in contact with ASN 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* 2.8 30.9 + - - +
36A GLU* 3.2 9.1 + - - +
38A MET* 1.3 74.5 - - - +
40A LYS* 1.3 64.7 + - + +
42A ARG* 2.9 34.7 + - - +
43A MET* 3.1 27.6 + - + +
135A PHE* 3.5 32.1 - - + -
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Residues in contact with LYS 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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36A GLU* 3.1 21.7 + - - +
37A GLU* 3.2 24.8 + - - +
39A ASN* 1.3 76.8 - - + +
41A LEU* 1.3 63.7 + - + +
43A MET* 3.4 8.5 + - - +
44A TYR* 3.0 27.1 + - - +
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Residues in contact with LEU 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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10A LYS 3.7 23.6 - - - +
11A ILE 4.8 1.3 - - - +
12A GLY* 5.2 5.6 - - - -
16A GLU* 4.2 11.7 - - + -
17A PHE* 3.7 33.4 - - + +
37A GLU* 2.9 33.2 - - - +
38A MET* 3.4 25.6 - - + +
39A ASN 3.2 0.4 - - - -
40A LYS* 1.3 79.8 - - + +
42A ARG* 1.3 64.4 + - - +
44A TYR* 3.3 9.5 + - + +
45A MET* 2.9 30.2 + - + +
61A LEU* 3.7 10.5 - - + -
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Residues in contact with ARG 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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35A GLU* 4.3 2.0 + - - -
38A MET* 3.0 21.2 + - - +
39A ASN* 2.9 34.7 + - - +
41A LEU* 1.3 76.8 - - - +
43A MET* 1.3 63.0 + - - +
45A MET* 3.2 8.1 + - - +
46A VAL* 3.0 26.9 + - - +
61A LEU* 3.4 31.2 + - + +
63A TYR* 3.0 39.2 + - - -
128A LYS* 6.1 4.2 - - - +
132A ASP* 2.8 30.6 + - - +
135A PHE* 3.8 17.2 - - + -
136A PHE* 3.7 20.0 - - + -
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Residues in contact with MET 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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39A ASN 3.1 12.6 + - - +
40A LYS* 3.7 9.4 - - - +
42A ARG* 1.3 79.3 - - - +
44A TYR* 1.3 58.1 + - - +
46A VAL* 3.3 5.1 + - + +
47A GLU* 2.9 33.7 + - + +
135A PHE* 4.3 24.0 - - + -
136A PHE* 4.5 9.6 - - - -
139A LYS* 4.8 13.7 - - + -
141A ILE* 4.1 24.5 - - + -
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Residues in contact with TYR 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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8A PHE* 3.8 14.0 - + - -
9A PRO 5.0 1.3 - - - -
10A LYS 6.1 0.7 - - - -
12A GLY* 4.5 23.1 - - - -
13A GLU* 3.0 33.6 + - + +
40A LYS 3.0 15.0 + - - +
41A LEU* 3.5 14.6 - - + +
43A MET* 1.3 77.9 - - - +
45A MET* 1.3 64.9 + - + +
47A GLU* 4.0 4.5 - - + +
48A ASN* 2.7 56.5 + - - -
316A VAL* 3.1 24.2 - - + +
336A LYS* 4.0 7.3 - - - -
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Residues in contact with MET 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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8A PHE* 3.2 39.2 - - + +
9A PRO 3.8 13.0 - - - +
10A LYS* 3.8 28.5 - - + +
41A LEU* 2.9 21.7 + - + +
42A ARG* 3.6 5.8 - - - +
44A TYR* 1.3 83.5 - - + +
46A VAL* 1.3 62.8 + - + +
48A ASN* 3.2 5.9 + - - +
49A TYR* 3.1 33.2 + - + -
60A GLU* 4.0 34.1 - - + +
61A LEU* 4.3 17.9 - - - +
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Residues in contact with VAL 46 (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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42A ARG 3.0 11.9 + - - +
43A MET* 3.9 7.9 - - + +
45A MET* 1.3 78.0 - - + +
47A GLU* 1.3 59.8 + - - +
49A TYR* 3.4 8.2 + - + +
50A ARG* 2.9 32.0 + - + +
56A ILE* 3.7 21.8 - - + +
57A PRO 4.4 6.5 - - - +
136A PHE* 3.3 38.4 - - + -
141A ILE* 3.5 38.6 - - + -
143A THR* 4.9 0.2 - - + -
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Residues in contact with GLU 47 (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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43A MET* 2.9 19.0 + - + +
44A TYR* 4.0 6.5 - - + +
46A VAL* 1.3 78.9 - - - +
48A ASN* 1.3 64.0 + - - +
50A ARG* 3.9 5.5 - - - +
51A LYS* 3.1 25.8 + - - +
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Residues in contact with ASN 48 (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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8A PHE* 3.8 15.9 - - + -
44A TYR* 2.7 55.2 + - - -
45A MET 3.2 9.0 + - - +
47A GLU* 1.3 80.6 - - - +
49A TYR* 1.3 59.9 + - - +
51A LYS* 3.6 3.4 + - - -
52A ASN* 3.0 30.5 + - - +
336A LYS* 3.2 27.9 + - - +
339A LEU* 3.5 18.9 - - + +
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Residues in contact with TYR 49 (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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5A ALA* 3.5 40.2 - - + -
6A PHE* 3.5 1.2 - - - -
7A GLY 3.3 6.2 + - - -
8A PHE* 3.0 38.9 + - + -
45A MET* 3.1 34.5 + - + -
46A VAL* 3.7 9.0 - - + +
48A ASN* 1.3 74.3 - - - +
50A ARG* 1.3 58.8 + - - +
52A ASN 2.8 4.7 + - - -
53A VAL* 2.7 43.7 + - + +
56A ILE* 4.3 15.3 - - + -
57A PRO* 3.6 24.7 - - + -
60A GLU* 2.6 29.6 + - - -
339A LEU* 4.3 11.2 - - + -
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Residues in contact with ARG 50 (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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46A VAL* 2.9 21.6 + - + +
47A GLU* 3.9 7.4 - - - +
49A TYR* 1.3 77.0 - - - +
51A LYS* 1.3 60.4 + - - +
52A ASN 3.2 1.6 + - - -
53A VAL 3.8 11.9 + - - +
56A ILE* 4.3 14.3 - - + +
141A ILE* 6.3 1.1 - - + -
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Residues in contact with LYS 51 (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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47A GLU 3.1 18.0 + - - +
48A ASN* 4.0 1.8 - - - +
49A TYR 3.1 0.6 + - - -
50A ARG* 1.3 76.0 - - - +
52A ASN* 1.3 76.7 + - - +
343A LYS* 4.2 13.7 - - - +
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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