Contacts of the helix formed by residues 17 - 32 (chain B) in PDB entry 1SXQ
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 17 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B ASN 4.7 3.1 + - - -
14B ASN* 4.4 1.2 + - - +
15B PHE 4.5 0.7 - - - -
16B LYS* 1.3 89.3 - - + +
18B VAL* 1.3 59.9 + - - +
19B PRO* 3.9 9.3 - - - +
20B SER* 3.0 24.8 + - - -
21B SER* 2.9 31.1 + - - -
237B LYS* 4.1 14.4 - - - +
240B MET 6.0 0.7 - - - -
10D T 5.7 1.6 - - - -
11D T 4.4 14.1 - - - +
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Residues in contact with VAL 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B THR* 1.3 69.8 - - - +
19B PRO* 1.3 76.1 - - + +
21B SER* 3.2 5.9 + - - -
22B GLU* 2.9 46.6 + - + +
215B ASN* 5.8 6.1 - - - +
237B LYS* 6.2 3.8 - - + +
238B ILE 5.5 0.7 - - - +
240B MET* 4.9 5.8 - - - +
400B UDP 3.5 53.2 - - + +
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Residues in contact with PRO 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ASN* 3.6 9.4 + - - +
10B ASN* 3.4 46.4 - - + +
17B THR* 3.6 11.7 - - - +
18B VAL* 1.3 96.1 - - + +
20B SER* 1.3 59.9 + - - +
22B GLU* 3.6 10.8 + - - +
23B THR* 2.8 29.5 + - - -
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Residues in contact with SER 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ASN 3.9 16.9 + - - -
12B VAL* 3.5 10.7 - - - +
13B ILE* 2.9 25.2 + - - -
14B ASN* 2.6 24.0 + - - -
17B THR* 3.0 22.3 + - - -
18B VAL 3.2 0.2 - - - -
19B PRO* 1.3 77.1 - - - +
21B SER* 1.3 67.0 + - - +
23B THR* 3.2 4.0 + - - -
24B ILE* 3.0 26.5 + - - +
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Residues in contact with SER 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ASN 3.7 1.3 + - - -
15B PHE* 3.2 43.8 + - - +
17B THR 2.9 23.2 + - - -
18B VAL 3.6 4.3 - - - -
20B SER* 1.3 76.1 - - - +
22B GLU* 1.3 57.7 + - - +
24B ILE* 3.2 2.4 + - - +
25B TYR* 2.8 35.9 + - - -
240B MET* 3.6 30.2 - - - +
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Residues in contact with GLU 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ASN* 5.5 0.2 + - - -
18B VAL* 2.9 35.1 + - + +
19B PRO* 3.9 9.8 - - - +
21B SER* 1.3 75.1 - - - +
23B THR* 1.3 59.3 + - - +
25B TYR* 3.7 4.3 - - - +
26B LEU* 3.0 42.2 + - + +
65B VAL* 4.6 13.6 - - + +
66B ASN* 5.4 1.7 + - - -
99B THR* 4.7 12.2 + - - -
165B TYR* 3.4 23.8 - - + +
240B MET* 4.1 11.0 - - + -
268B LEU* 3.9 14.2 - - - +
400B UDP 5.8 1.0 - - - +
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Residues in contact with THR 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B ILE* 4.5 8.8 - - + +
6B ILE 4.5 2.7 - - - -
7B ASN* 3.2 30.0 + - - +
12B VAL* 3.9 21.5 - - + +
19B PRO 2.8 20.4 + - - -
20B SER 3.2 5.4 + - - -
22B GLU* 1.3 77.2 - - - +
24B ILE* 1.3 58.5 + - - +
26B LEU* 3.4 3.6 + - - +
27B PHE* 3.0 26.5 + - - +
39B ILE* 4.2 18.4 - - + -
65B VAL* 4.0 22.7 - - + +
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Residues in contact with ILE 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B VAL* 3.8 14.4 - - + -
13B ILE 3.8 4.0 - - - +
14B ASN* 3.6 33.4 - - - +
15B PHE* 3.5 26.5 - - + -
20B SER* 3.0 16.8 + - - +
21B SER 3.7 3.1 - - - +
23B THR* 1.3 73.2 - - - +
25B TYR* 1.3 60.3 + - - +
27B PHE* 3.2 3.1 + - + +
28B LYS* 2.8 41.3 + - + +
39B ILE* 3.9 12.1 - - + -
47B TYR* 3.6 39.0 - - + -
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Residues in contact with TYR 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B PHE* 3.9 25.8 - + - -
21B SER 2.8 25.7 + - - +
22B GLU 3.7 2.5 - - - +
24B ILE* 1.3 75.8 - - - +
26B LEU* 1.3 59.3 + - - +
28B LYS* 3.2 11.3 + - + +
29B VAL* 2.8 31.5 + - - +
165B TYR* 3.5 22.9 - + + -
166B LYS* 5.2 12.4 + - + -
169B MET* 3.9 31.2 - - + +
171B ASP* 5.6 5.6 - - - -
240B MET* 3.6 41.0 + - + -
241B ASN* 3.1 32.1 - - + +
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Residues in contact with LEU 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B ILE* 3.7 12.3 - - + -
22B GLU* 3.0 24.6 + - + +
23B THR 3.7 4.3 - - - +
25B TYR* 1.3 76.4 - - - +
27B PHE* 1.3 63.3 + - - +
29B VAL* 3.2 11.2 - - + +
30B ILE* 2.9 37.5 + - + +
65B VAL* 3.7 31.4 - - + -
97B LEU* 3.8 18.2 - - + -
99B THR* 5.7 3.1 - - + -
162B ILE* 3.9 15.7 - - + +
165B TYR* 3.6 34.3 - - + -
341B TRP* 6.3 0.2 - - + -
345B PHE* 5.9 4.3 - - + -
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Residues in contact with PHE 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B ILE* 4.4 9.3 - - + +
23B THR 3.0 6.3 + - - +
24B ILE* 3.2 15.2 + - + +
26B LEU* 1.3 76.9 - - - +
28B LYS* 1.3 70.9 + - + +
30B ILE* 4.7 3.6 - - - -
31B SER* 2.8 46.9 + - - -
37B VAL* 3.2 40.6 - - + +
38B ASP* 4.4 4.0 - - - -
39B ILE* 3.4 42.4 - - + -
47B TYR* 4.4 26.0 - + - -
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Residues in contact with LYS 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B PHE* 4.0 14.4 - - + -
24B ILE* 2.8 38.3 + - + +
25B TYR* 3.5 12.8 - - + +
27B PHE* 1.3 87.6 - - + +
29B VAL* 1.3 62.1 + - - +
31B SER* 3.2 5.7 + - - -
32B GLU* 2.8 41.5 + - - +
47B TYR* 4.2 20.4 + - - -
169B MET* 3.6 16.6 - - + -
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Residues in contact with VAL 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B TYR 2.8 19.1 + - - +
26B LEU* 3.2 21.8 - - + +
28B LYS* 1.3 73.2 - - - +
30B ILE* 1.3 71.7 + - + +
32B GLU* 3.3 8.3 + - + +
33B MET* 3.3 25.3 + - + +
165B TYR* 4.0 17.0 - - + +
168B HIS* 4.7 10.8 - - + +
169B MET* 3.7 23.5 - - + +
338B LYS* 6.1 1.8 - - - -
341B TRP* 3.6 34.8 - - + -
342B GLN* 5.3 2.0 + - - +
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Residues in contact with ILE 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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3B ILE* 4.4 6.3 - - + -
5B ILE* 4.3 13.7 - - + -
26B LEU* 2.9 29.0 + - + +
27B PHE* 3.8 4.7 - - - +
29B VAL* 1.3 79.6 - - + +
31B SER* 1.3 65.4 + - - +
33B MET* 3.0 25.5 + - + +
35B LEU* 3.4 32.8 + - + -
37B VAL* 3.7 25.1 - - + -
63B ILE* 3.8 17.3 - - + -
97B LEU* 5.9 0.9 - - + -
345B PHE* 3.7 34.1 - - + -
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Residues in contact with SER 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B PHE* 2.8 37.9 + - - -
28B LYS* 3.5 7.9 - - - -
30B ILE* 1.3 76.0 - - - +
32B GLU* 1.3 59.6 + - - +
34B GLY* 3.1 20.3 + - - -
35B LEU 3.5 14.6 + - - +
37B VAL* 3.2 14.8 + - - +
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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
----------------------------------------------------------
28B LYS* 2.8 25.4 + - + +
29B VAL* 3.7 8.5 - - + +
30B ILE 3.1 0.6 - - - -
31B SER* 1.3 75.2 - - - +
33B MET* 1.3 55.9 + - - +
34B GLY 3.1 6.6 + - - -
168B HIS 4.2 1.9 - - - +
169B MET* 3.7 20.8 - - - +
170B ASN* 2.9 61.4 + - - +
171B ASP* 5.1 1.0 + - - +
338B LYS* 5.6 1.7 + - - +
342B GLN* 4.0 10.3 + - - +
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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
------------------------------------------------------------
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