Contacts of the helix formed by residues 22 - 35 (chain B) in PDB entry 1XT9
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 22 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20B THR 3.6 1.9 + - - +
21B ASP* 1.3 78.1 - - - +
23B VAL* 1.3 66.6 + - - +
24B GLU* 2.9 21.0 + - + +
25B ARG* 3.0 20.4 + - + +
26B ILE* 3.2 11.2 + - - +
52B ASP 3.4 13.0 - - - +
53B GLU* 3.3 49.0 + - - +
54B LYS 3.3 6.5 - - - +
55B THR* 4.0 10.1 - - + +
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Residues in contact with VAL 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B LYS* 1.3 73.7 - - - +
24B GLU* 1.3 62.8 + - - +
26B ILE* 3.0 17.7 + - + +
27B LYS* 2.9 35.1 + - - +
43B LEU* 4.2 11.7 - - + -
50B MET* 4.0 21.1 - - + +
51B ASN 3.3 11.2 - - - +
52B ASP* 3.2 28.7 + - - +
54B LYS 2.9 21.3 + - - +
55B THR 4.9 1.8 - - - +
56B ALA* 5.9 0.2 - - - -
59B TYR* 3.9 22.9 - - + -
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Residues in contact with GLU 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ARG* 4.4 18.2 + - - +
22B LYS* 2.9 16.1 + - + +
23B VAL* 1.3 78.3 - - - +
25B ARG* 1.3 60.1 + - - +
27B LYS* 3.4 7.0 + - - +
28B GLU* 3.0 42.5 + - + +
38B PRO* 4.9 4.6 - - + +
52B ASP* 3.0 33.6 + - + +
53B GLU* 4.3 13.9 - - - +
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Residues in contact with ARG 25 (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 ILE* 5.8 0.7 - - + -
21B ASP* 3.9 39.0 + - + +
22B LYS* 3.0 18.4 + - + +
24B GLU* 1.3 76.7 + - - +
26B ILE* 1.3 66.1 + - - +
28B GLU* 3.3 27.4 + - - +
29B ARG* 3.1 39.9 + - + +
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Residues in contact with ILE 26 (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 ILE* 4.9 4.0 - - + -
5B VAL* 5.0 1.8 - - + -
15B ILE* 4.7 15.0 - - + -
17B ILE* 4.1 29.4 - - + -
21B ASP* 4.7 3.6 - - + +
22B LYS 3.2 9.4 + - - +
23B VAL* 3.0 32.9 + - + +
25B ARG* 1.3 78.5 - - - +
27B LYS* 1.3 63.0 + - - +
29B ARG* 3.0 19.1 + - - +
30B VAL* 3.1 20.5 + - + +
43B LEU* 3.6 20.4 - - + -
50B MET* 5.7 1.3 - - - -
56B ALA* 4.7 13.7 - - + -
61B ILE* 5.6 2.5 - - + -
67B LEU* 4.5 19.1 - - + -
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Residues in contact with LYS 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A HIS* 5.4 4.2 - - - -
23B VAL* 2.9 24.7 + - - +
24B GLU* 3.7 8.1 - - - +
25B ARG 3.4 0.2 - - - -
26B ILE* 1.3 74.7 - - - +
28B GLU* 1.3 57.1 + - - +
30B VAL* 3.0 3.7 - - - +
31B GLU* 3.0 13.7 + - - +
38B PRO* 3.7 31.9 - - + +
41B GLN* 2.8 68.4 + - + +
42B ARG* 3.7 9.7 - - - +
43B LEU* 3.9 22.5 - - + +
50B MET 4.3 6.4 + - - -
52B ASP* 2.6 38.0 + - - +
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Residues in contact with GLU 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B GLU* 3.0 28.8 - - + +
25B ARG* 3.3 38.0 + - - +
26B ILE 3.1 0.6 - - - -
27B LYS* 1.3 73.0 - - - +
29B ARG* 1.3 66.8 + - + +
30B VAL 3.0 1.6 - - - -
31B GLU* 3.0 18.9 + - - +
32B GLU* 3.0 23.9 + - - +
38B PRO* 4.1 21.2 - - + +
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Residues in contact with ARG 29 (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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15B ILE* 3.3 29.6 - - + +
16B ASP* 3.1 46.8 + - - +
17B ILE* 4.4 5.4 - - + -
25B ARG* 3.1 29.2 - - + +
26B ILE* 3.0 7.6 + - - +
28B GLU* 1.3 76.0 - - - +
30B VAL* 1.3 60.8 + - - +
32B GLU* 3.4 44.1 + - - +
33B LYS* 3.7 6.2 + - - +
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Residues in contact with VAL 30 (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 VAL* 4.3 29.2 - - + -
13B ILE* 5.1 6.3 - - + -
15B ILE* 4.1 11.4 - - + -
26B ILE* 3.1 19.7 + - + +
27B LYS* 3.0 12.6 - - - +
28B GLU 3.0 0.4 - - - -
29B ARG* 1.3 76.4 - - - +
31B GLU* 1.3 62.9 + - - +
33B LYS* 3.0 5.9 + - - +
34B GLU* 2.9 31.3 + - + +
36B ILE* 5.2 1.8 - - + -
41B GLN* 3.1 27.1 - - - +
43B LEU* 5.0 3.1 - - + -
69B LEU* 4.1 17.5 - - + -
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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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27B LYS 3.0 9.7 + - - +
28B GLU* 3.0 14.9 + - - +
30B VAL* 1.3 75.7 - - - +
32B GLU* 1.3 62.3 + - - +
35B GLY* 2.8 29.2 + - - -
36B ILE 3.1 32.5 - - - +
37B PRO* 3.6 10.9 - - - +
38B PRO* 3.5 27.7 - - + +
41B GLN* 4.2 0.2 - - - +
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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
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28B GLU* 3.0 18.0 + - - +
29B ARG* 3.4 50.0 + - - +
30B VAL 3.1 0.2 - - - -
31B GLU* 1.3 79.5 - - + +
33B LYS* 1.3 62.2 + - + +
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Residues in contact with LYS 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ILE* 4.3 19.3 - - + -
14B GLU* 2.7 35.0 + - - +
15B ILE* 4.3 5.8 - - + +
29B ARG 3.7 6.9 + - - +
30B VAL 3.0 6.7 + - - +
32B GLU* 1.3 85.3 - - + +
34B GLU* 1.3 65.2 + - + +
35B GLY 3.6 1.3 - - - -
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Residues in contact with GLU 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B THR* 5.4 1.8 - - - -
11B LYS* 4.3 25.4 + - - +
13B ILE* 3.8 36.3 - - + +
30B VAL* 2.9 18.7 + - + +
33B LYS* 1.3 84.0 - - + +
35B GLY* 1.3 67.0 + - - +
36B ILE* 3.0 27.5 + - + +
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Residues in contact with GLY 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* 2.8 22.1 + - - -
33B LYS 3.6 1.4 - - - -
34B GLU* 1.3 78.0 - - - +
36B ILE* 1.3 60.8 + - - +
37B PRO* 3.8 8.0 - - - +
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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
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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