Contacts of the helix formed by residues 34 - 49 (chain A) in PDB entry 1XHU
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 GLY 34 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A ALA* 1.3 80.3 - - - +
35A GLU* 1.3 67.9 + - - +
36A PRO* 3.3 5.4 - - - -
37A PHE* 3.0 43.9 + - - +
38A GLU 3.7 2.1 + - - -
130A THR* 3.5 20.7 + - - +
173A TRP* 4.0 2.6 - - - +
180A LEU* 4.2 1.1 - - - -
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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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23A PRO* 5.9 0.9 - - + -
31A HIS 4.5 17.0 - - - +
32A ALA* 4.3 9.8 - - - +
33A ALA 3.4 2.6 - - - -
34A GLY* 1.3 73.9 - - - +
36A PRO* 1.3 75.5 - - + +
38A GLU* 2.9 35.1 + - - +
39A LYS* 3.4 30.2 + - - +
24B LYS* 4.9 11.9 - - + -
26B GLY* 5.5 2.6 - - - -
27B THR* 5.3 9.5 + - - -
8H G 5.3 4.0 + - - -
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Residues in contact with PRO 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A VAL* 3.6 39.6 - - + +
21A LYS 4.3 9.0 - - - +
23A PRO* 4.7 10.5 - - + -
33A ALA 4.7 3.1 - - - +
34A GLY* 3.3 7.0 - - - -
35A GLU* 1.3 97.9 - - + +
37A PHE* 1.3 55.4 + - - +
39A LYS* 3.3 16.0 + - + +
40A LEU* 2.9 27.2 + - - +
180A LEU* 5.1 0.4 - - + -
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Residues in contact with PHE 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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15A LEU* 5.0 5.2 - - + -
18A GLN* 4.6 4.3 - - + -
20A VAL* 4.1 17.5 - - + -
34A GLY* 3.0 32.7 + - - +
35A GLU 3.0 0.6 + - - -
36A PRO* 1.3 73.3 - - + +
38A GLU* 1.3 55.9 + - - +
40A LEU* 2.7 18.2 - - + +
41A VAL* 2.7 39.9 + - + +
130A THR* 4.6 2.5 - - + -
171A VAL* 3.7 30.1 - - + -
173A TRP* 3.4 34.8 - + + -
180A LEU* 3.1 38.4 - - + -
182A CYS* 3.7 27.4 - - + -
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Residues in contact with GLU 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A GLY 3.7 3.2 + - - +
35A GLU* 2.9 23.3 + - - +
37A PHE* 1.3 79.2 - - - +
39A LYS* 1.3 62.3 + - - +
40A LEU 2.9 0.2 + - - -
41A VAL* 3.1 8.6 + - - +
42A TYR* 2.8 29.5 + - - +
55A LYS* 3.3 33.1 + - - -
114A ASP* 3.8 28.4 - - - +
115A ILE* 4.1 6.6 - - - +
128A VAL* 3.7 33.8 - - + +
130A THR* 5.3 1.7 - - + +
8H G 5.0 6.2 + - - +
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Residues in contact with LYS 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* 3.4 27.4 + - - +
36A PRO* 3.3 17.4 + - + +
38A GLU* 1.3 86.7 + - - +
40A LEU* 1.3 56.9 + - - +
42A TYR* 3.8 8.7 - - + +
43A LYS* 2.9 31.8 + - + +
55A LYS* 5.5 4.9 - - - +
24B LYS* 4.1 29.5 + - - +
26B GLY* 5.6 5.9 - - - -
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Residues in contact with LEU 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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14A ILE* 5.0 14.1 - - + +
15A LEU* 3.3 26.9 - - + -
18A GLN* 4.1 27.8 - - + -
20A VAL* 4.8 12.3 - - + -
36A PRO 2.9 12.7 + - - +
37A PHE* 2.7 21.4 + - + +
39A LYS* 1.3 75.4 - - - +
41A VAL* 1.3 61.9 + - - +
42A TYR 3.1 1.1 - - - -
43A LYS* 3.5 7.6 + - + +
44A PHE* 3.1 22.5 + - - +
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Residues in contact with VAL 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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4A ILE* 5.0 2.0 - - + -
11A ILE* 4.2 13.7 - - + -
15A LEU* 3.5 31.6 - - + -
37A PHE 2.7 24.0 + - - +
38A GLU* 3.7 7.6 - - - +
40A LEU* 1.3 71.6 - - - +
42A TYR* 1.3 64.4 + - - +
44A PHE* 3.3 8.3 + - - +
45A LEU* 3.1 34.8 + - + +
115A ILE* 5.1 4.9 - - + -
126A LEU* 5.1 1.1 - - + -
128A VAL* 5.1 9.0 - - + -
169A LEU* 3.5 29.6 - - + -
171A VAL* 4.4 4.9 - - + -
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Residues in contact with TYR 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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38A GLU* 2.8 17.2 + - - +
39A LYS* 3.8 9.4 - - + +
41A VAL* 1.3 74.6 - - - +
43A LYS* 1.3 80.6 + - + +
44A PHE 3.0 0.5 + - - -
45A LEU* 3.0 5.8 + - - +
46A LYS* 2.9 48.2 + - + +
53A THR* 4.0 17.5 - - + -
54A PHE 4.2 8.7 - - - -
55A LYS* 3.5 39.7 - - + +
58A GLU* 2.8 33.9 + - - -
115A ILE* 3.5 32.3 - - + +
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Residues in contact with LYS 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 LYS 2.9 21.9 + - - +
40A LEU* 4.1 9.4 - - + +
42A TYR* 1.3 85.6 - - + +
44A PHE* 1.3 64.6 + - - +
46A LYS* 3.4 9.4 + - + +
47A GLU* 3.2 30.2 + - + +
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Residues in contact with PHE 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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7A ILE* 4.1 6.1 - - + -
10A ASP* 3.7 30.1 - - + -
11A ILE* 3.0 34.8 - - + -
14A ILE* 3.8 33.7 - - + -
40A LEU 3.1 13.9 + - - +
41A VAL* 3.3 10.5 - - - +
42A TYR 3.0 0.6 + - - -
43A LYS* 1.3 77.5 - - - +
45A LEU* 1.3 85.3 + - + +
47A GLU* 2.9 15.1 + - + +
48A ASN* 2.9 55.4 + - - +
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Residues in contact with LEU 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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4A ILE* 3.5 26.5 - - + -
7A ILE* 4.2 4.3 - - + -
11A ILE* 3.5 19.7 - - + -
41A VAL* 3.1 16.1 + - + +
42A TYR 3.0 5.4 + - - +
44A PHE* 1.3 102.4 - - + +
46A LYS* 1.3 61.2 + - - +
48A ASN* 4.3 1.6 - - - +
49A LEU* 2.5 44.3 + - + +
53A THR* 3.5 15.9 - - + +
115A ILE* 4.0 28.3 - - + -
117A LEU* 4.7 4.5 - - + -
126A LEU* 4.0 5.4 - - + -
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Residues in contact with LYS 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 TYR* 2.9 48.0 + - + +
43A LYS* 3.7 17.0 - - + +
45A LEU* 1.3 76.4 - - - +
47A GLU* 1.3 58.1 + - - +
50A SER* 3.0 46.8 + - - +
53A THR* 3.0 37.7 + - - +
54A PHE* 5.7 2.4 - - - -
58A GLU* 3.4 10.8 - - - -
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Residues in contact with GLU 47 (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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43A LYS* 3.2 21.6 + - + +
44A PHE* 2.9 11.3 + - + +
46A LYS* 1.3 79.1 - - - +
48A ASN* 1.3 73.8 + - - +
50A SER* 4.2 7.8 - - - -
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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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7A ILE* 4.6 8.2 - - + +
10A ASP* 4.7 9.3 + - - +
44A PHE* 2.9 58.5 + - + +
45A LEU* 3.9 3.6 - - - +
47A GLU* 1.3 84.6 - - - +
49A LEU* 1.3 68.3 + - + +
50A SER* 2.9 10.5 + - - -
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Residues in contact with LEU 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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3A PHE* 3.2 40.2 - - + +
4A ILE* 4.5 2.2 - - - -
7A ILE* 3.6 29.8 - - + -
45A LEU* 2.5 17.9 + - + +
48A ASN* 1.3 77.2 - - + +
50A SER* 1.3 52.6 + - - -
51A ASP 2.8 16.8 + - - -
52A LEU* 2.9 32.5 + - + -
53A THR* 2.8 22.8 + - - +
117A LEU* 4.6 12.1 - - + -
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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