Contacts of the helix formed by residues 20 - 31 (chain B) in PDB entry 1SIW
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 HIS 20 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A PRO* 4.4 2.5 - - + -
1095A TRP* 3.4 29.6 - + + -
1110A LEU* 4.4 13.2 - - + +
18B GLY* 3.5 17.8 + - - -
19B CYS* 1.3 76.1 - - - +
21B THR* 1.3 65.3 + - - +
22B CYS 3.1 2.9 - - - -
23B SER* 2.9 23.2 + - - -
24B VAL* 3.1 12.3 + - - +
44B VAL* 3.2 51.6 + - + +
46B THR* 5.6 1.2 + - - -
143B ASN* 3.2 20.9 + - + -
146B ASP* 3.1 18.9 + - - -
179B TYR* 6.0 1.0 - - - -
802B SF4 3.1 14.5 - - - -
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Residues in contact with THR 21 (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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59A TRP* 4.7 0.2 - - + -
73A GLN* 4.0 9.4 - - - +
92A CYS 3.1 18.9 - - - +
93A PRO* 3.1 30.0 - - - +
96A ALA* 4.0 11.0 - - + -
19B CYS* 3.3 7.3 + - - -
20B HIS* 1.3 74.3 - - - +
22B CYS* 1.3 63.1 + - - +
24B VAL* 3.0 4.6 + - - +
25B THR* 3.0 29.8 + - + -
262B THR 3.7 15.3 - - - +
264B VAL* 3.4 23.8 - - + +
802B SF4 4.1 5.6 - - - -
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Residues in contact with CYS 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B HIS 4.3 1.3 - - - -
21B THR* 1.3 80.3 - - - +
23B SER* 1.3 61.4 + - - +
25B THR* 3.3 16.5 + - - -
26B CYS* 3.4 14.7 + - - +
42B ASN* 3.3 23.8 + - - +
44B VAL* 3.7 15.0 - - - -
259B CYS* 4.0 14.4 - - + +
262B THR* 4.1 7.2 + - - -
268B ARG* 3.1 30.5 - - - +
802B SF4 2.3 39.9 - - - -
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Residues in contact with SER 23 (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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1110A LEU* 5.0 2.5 - - - -
20B HIS* 2.9 20.5 + - - -
22B CYS* 1.3 78.9 - - - +
24B VAL* 1.3 65.5 + - - +
26B CYS* 3.6 2.3 + - - +
27B LYS* 3.1 23.9 + - - +
40B TRP* 3.8 19.4 - - - -
42B ASN* 2.9 37.2 + - - +
43B ASN* 3.5 9.8 - - - -
44B VAL* 3.7 12.3 + - - +
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Residues in contact with VAL 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A PRO* 4.2 8.3 - - + +
96A ALA* 3.5 38.6 - - + +
97A SER* 3.8 11.2 - - - +
1106A LEU* 4.3 9.6 - - + -
1107A MET* 4.0 15.3 - - + -
1110A LEU* 3.7 25.8 - - + -
20B HIS 3.6 11.2 - - - +
21B THR 3.0 7.0 + - - +
23B SER* 1.3 74.3 - - - +
25B THR* 1.3 60.2 + - - +
27B LYS* 3.2 7.2 + - - +
28B ASN* 2.9 32.8 + - - +
40B TRP* 4.7 2.2 - - + -
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Residues in contact with THR 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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59A TRP* 4.8 0.7 - - + -
71A GLU 4.1 16.4 - - - +
72A THR* 5.1 0.7 - - - -
73A GLN* 4.5 2.9 - - - +
96A ALA* 3.9 20.0 - - + +
21B THR* 3.0 14.4 + - + +
22B CYS 3.3 8.7 + - - -
24B VAL* 1.3 76.1 - - - +
26B CYS* 1.3 64.0 + - - +
28B ASN* 3.5 7.2 + - - +
29B VAL* 3.2 28.8 + - - +
258B VAL* 3.5 20.7 + - - +
262B THR* 2.9 37.0 + - + +
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Residues in contact with CYS 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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22B CYS 3.4 14.6 + - - +
23B SER 3.9 3.6 - - - +
24B VAL 3.3 0.8 - - - -
25B THR* 1.3 79.8 + - - +
27B LYS* 1.3 65.2 + - - +
29B VAL 3.2 1.0 + - - -
30B TRP* 2.9 38.3 + - - +
31B THR* 3.9 1.7 + - - -
41B PHE* 3.6 27.8 - - - -
42B ASN* 4.2 9.6 - - + +
258B VAL* 4.5 1.3 - - - +
803B SF4 2.3 44.9 - - - -
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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
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1106A LEU* 3.6 27.1 - - + -
23B SER 3.1 16.4 + - - +
24B VAL* 3.2 5.6 + - - +
26B CYS* 1.3 79.8 - - - +
28B ASN* 1.3 62.0 + - - +
31B THR* 2.8 60.5 + - - +
32B SER* 2.8 23.6 + - - +
36B VAL 3.2 2.4 + - - -
37B GLU* 2.9 25.2 + - - +
39B ALA 2.6 26.6 + - - -
40B TRP* 3.8 27.8 - - + +
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Residues in contact with ASN 28 (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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38A ARG* 3.3 17.0 + - - -
69A THR 4.6 5.4 - - - +
70A TRP* 3.9 19.8 - - + -
71A GLU* 3.5 10.7 + - - +
96A ALA 2.7 29.9 + - - -
97A SER* 4.3 1.4 - - - +
99A SER* 3.8 10.8 + - - -
100A TRP* 5.8 0.3 + - - -
1106A LEU* 3.4 22.6 - - - +
24B VAL* 2.9 24.5 + - - +
25B THR* 3.8 7.4 - - - +
27B LYS* 1.3 77.3 - - - +
29B VAL* 1.3 62.3 + - - +
32B SER* 3.6 14.3 + - - -
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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
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38A ARG* 2.9 33.1 + - + +
39A TRP* 4.0 20.4 - - + -
70A TRP* 3.8 45.5 - - + +
72A THR* 5.4 0.4 - - + -
25B THR 3.2 15.7 + - - +
26B CYS* 3.2 3.2 + - - +
28B ASN* 1.3 78.3 - - - +
30B TRP* 1.3 98.9 + - + +
32B SER 5.4 0.6 + - - -
258B VAL* 4.6 9.9 - - + -
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Residues in contact with TRP 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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35A TYR* 3.4 53.9 - + + -
38A ARG* 4.1 16.8 - - + -
39A TRP* 3.8 25.1 - + + -
26B CYS* 2.9 27.5 + - - +
29B VAL* 1.3 97.5 - - + +
31B THR* 1.3 59.5 + - + +
32B SER 3.8 1.6 - - - -
33B ARG* 3.0 29.8 + - - -
41B PHE* 4.2 18.4 - - + -
245B ILE* 3.9 15.5 - - + -
247B CYS* 3.5 35.2 - - + -
249B PRO* 3.9 13.9 - - + -
250B ARG* 5.8 0.9 - - + -
258B VAL* 4.6 2.0 - - - +
803B SF4 3.7 18.6 - - - -
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Residues in contact with THR 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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26B CYS* 3.9 2.0 + - - +
27B LYS* 2.8 60.8 + - - +
30B TRP* 1.3 82.2 - - + +
32B SER* 1.3 60.9 + - - +
33B ARG* 3.3 3.3 + - - +
36B VAL* 3.3 26.6 - - + +
37B GLU* 3.8 2.9 - - - -
39B ALA* 3.2 8.1 + - + +
40B TRP* 5.0 1.0 - - - -
41B PHE* 3.5 47.4 + - + +
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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