Contacts of the helix formed by residues 26 - 42 (chain B) in PDB entry 5TWV
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 CYS 26 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A PHE* 3.8 23.4 - - + -
6B CYS* 2.0 54.4 - - + -
11B HIS* 5.8 4.7 - - - -
15B TYR* 5.5 4.0 - - - +
25B GLY* 1.3 78.3 - - - +
27B PHE* 1.3 64.3 + - - +
28B VAL 3.4 2.7 - - - -
29B ASP* 3.4 9.9 + - - +
30B ALA* 3.2 21.1 + - - +
105B HIS* 5.0 3.3 - - + +
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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
----------------------------------------------------------
92A LEU* 5.8 5.8 - - + +
95A PHE* 4.6 13.9 - - + +
21B VAL* 4.0 30.1 - - + +
24B ASN* 4.1 8.5 - - + -
25B GLY 3.5 0.4 - - - -
26B CYS* 1.3 75.5 - - - +
28B VAL* 1.3 58.9 + - - +
29B ASP 3.1 2.5 - - - -
30B ALA* 3.8 7.4 - - - +
31B LEU* 2.9 31.7 + - - +
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Residues in contact with VAL 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ASN* 3.4 33.8 + - + +
25B GLY 5.2 1.1 - - - +
26B CYS 3.4 0.6 - - - -
27B PHE* 1.3 78.6 - - - +
29B ASP* 1.3 60.6 + - - +
31B LEU* 4.0 7.1 - - - +
32B ASN* 3.8 13.0 + - - +
149B THR* 4.8 4.7 - - - +
152B ILE* 3.6 20.2 - - + -
153B LYS* 3.6 28.4 + - + +
156B LYS* 5.5 2.2 - - + -
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Residues in contact with ASP 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B GLY 5.4 1.1 + - - +
26B CYS* 3.4 12.4 + - - +
27B PHE 3.1 0.4 - - - -
28B VAL* 1.3 78.7 - - - +
30B ALA* 1.3 62.5 + - - +
31B LEU 3.2 1.3 + - - -
32B ASN* 3.4 6.2 + - - +
33B VAL* 3.4 10.7 + - - +
105B HIS* 3.4 26.9 - - + +
106B LEU* 5.4 1.1 - - - +
109B PRO* 3.3 32.6 - - + +
153B LYS* 4.2 7.6 - - - +
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Residues in contact with ALA 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A MET* 5.3 5.1 - - - +
91A TRP* 4.3 25.6 - - + -
92A LEU* 4.8 19.2 - - + +
95A PHE* 5.4 7.0 - - + -
26B CYS 3.2 14.1 + - - +
27B PHE* 3.3 7.4 + - - +
29B ASP* 1.3 78.7 - - - +
31B LEU* 1.3 63.8 + - - +
33B VAL* 3.5 20.1 + - - +
34B VAL* 3.8 7.6 + - - +
105B HIS* 6.0 3.3 - - + +
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Residues in contact with LEU 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A LEU* 5.4 15.5 - - + +
27B PHE 2.9 18.0 + - - +
28B VAL* 4.0 6.1 - - - +
29B ASP 3.2 0.2 - - - -
30B ALA* 1.3 79.2 - - - +
32B ASN* 1.3 60.4 + - - +
34B VAL* 3.7 4.1 + - + +
35B PRO* 3.2 22.7 - - + +
148B ILE* 5.1 1.8 - - + +
149B THR* 3.8 18.0 - - + +
152B ILE* 4.0 30.5 - - + -
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Residues in contact with ASN 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B VAL 3.8 9.8 + - - +
29B ASP 3.4 10.0 + - - +
31B LEU* 1.3 80.0 - - - +
33B VAL* 1.3 61.1 + - - +
34B VAL 3.5 0.5 + - - -
35B PRO* 3.5 14.6 - - - +
36B HIS* 3.8 8.7 + - - +
109B PRO* 4.4 16.2 - - + +
142B TYR* 5.5 0.9 + - - -
149B THR* 3.8 24.4 - - - +
153B LYS* 4.9 8.7 - - - -
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Residues in contact with VAL 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A MET* 3.7 30.1 - - + -
29B ASP 3.4 16.8 - - - +
30B ALA* 3.7 11.7 - - - +
31B LEU 3.3 0.8 - - - -
32B ASN* 1.3 75.6 - - - +
34B VAL* 1.3 64.9 + - - +
36B HIS* 3.2 8.5 + - - +
37B VAL* 3.1 21.0 + - + +
108B MET* 4.6 10.8 - - + +
109B PRO* 4.2 24.9 - - + -
112B MET* 4.8 12.3 - - + -
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Residues in contact with VAL 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A LEU* 5.0 5.6 - - + +
88A MET* 4.5 21.0 - - + +
92A LEU* 5.7 9.0 - - + -
30B ALA 3.8 6.1 + - - +
31B LEU* 3.7 7.4 + - + +
33B VAL* 1.3 78.4 - - - +
35B PRO* 1.3 69.1 - - + +
37B VAL* 3.3 6.1 + - - +
38B PHE* 3.0 28.8 + - - +
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Residues in contact with PRO 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LEU* 3.2 15.5 - - + +
32B ASN* 3.5 11.9 - - - +
34B VAL* 1.3 99.4 - - + +
36B HIS* 1.3 57.9 + - - +
38B PHE* 3.2 8.5 + - + +
39B LEU 2.9 24.3 + - - -
142B TYR* 3.3 26.6 - - + -
145B LEU* 4.1 44.6 - - + +
146B ALA* 5.2 2.9 - - - +
149B THR* 4.9 1.8 - - + -
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Residues in contact with HIS 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B ASN 3.8 7.6 + - - +
33B VAL 3.2 8.8 + - - +
35B PRO* 1.3 78.4 - - - +
37B VAL* 1.3 62.4 - - - +
39B LEU* 3.3 3.3 + - - +
40B LEU* 3.0 24.4 + - - +
112B MET* 3.7 36.3 - - + +
113B ALA 4.7 0.4 - - - +
116B ALA* 4.2 6.5 - - + +
142B TYR* 3.4 24.6 - - - +
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Residues in contact with VAL 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A LEU* 5.3 2.5 - - + -
88A MET* 5.3 11.4 - - + -
33B VAL* 3.1 16.6 + - + +
34B VAL* 3.6 10.1 - - - +
35B PRO 3.3 0.2 - - - -
36B HIS* 1.3 76.2 - - - +
38B PHE* 1.3 51.4 + - - +
40B LEU* 3.1 3.3 + - - +
41B PHE* 2.7 75.8 + - + -
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Residues in contact with PHE 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A LEU* 4.4 28.0 - - + +
34B VAL 3.0 13.9 + - - +
35B PRO* 3.5 11.4 - - + +
37B VAL* 1.3 78.5 - - - +
39B LEU* 1.3 66.0 + - + +
41B PHE* 4.0 7.3 - - - +
42B ILE* 3.2 35.4 + - + +
138B ALA* 5.2 16.4 - - + -
141B ILE* 5.5 8.5 - - + -
142B TYR* 6.1 2.2 - + + -
145B LEU* 6.1 6.3 - - + -
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Residues in contact with LEU 39 (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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35B PRO 2.9 16.3 + - - +
36B HIS 3.7 4.7 - - - +
38B PHE* 1.3 81.0 - - + +
40B LEU* 1.3 57.4 + - - +
42B ILE* 4.4 3.3 - - - +
43B THR* 3.5 20.3 + - - -
116B ALA* 5.0 8.3 - - + +
119B THR* 4.7 6.6 - - - -
123B TYR* 4.4 8.2 - - - -
138B ALA 5.7 2.7 - - - +
139B LEU* 6.4 1.8 - - + -
142B TYR* 3.5 29.2 - - + -
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Residues in contact with LEU 40 (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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36B HIS 3.0 15.3 + - - +
37B VAL* 3.1 6.3 + - - +
39B LEU* 1.3 80.0 - - - +
41B PHE* 1.3 66.4 + - + +
42B ILE 3.5 0.4 - - - -
43B THR* 4.0 5.2 - - - -
44B PHE* 3.3 45.7 + - + -
115B MET* 5.9 5.2 - - + +
116B ALA* 5.6 6.3 - - - +
119B THR* 5.2 9.6 - - - -
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Residues in contact with PHE 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A SER* 5.8 0.2 - - - -
81A CYS* 3.3 49.2 - - + +
84A LEU* 3.7 27.4 - - + -
85A LEU* 3.9 26.2 - - + -
37B VAL* 2.7 49.8 + - + +
38B PHE* 4.0 6.3 - - - +
40B LEU* 1.3 87.6 - - + +
42B ILE* 1.3 62.6 + - - +
43B THR 3.4 0.4 - - - -
44B PHE* 4.6 8.3 - + - -
45B PRO* 3.7 16.5 - - - +
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Residues in contact with ILE 42 (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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38B PHE* 3.2 30.6 + - + +
39B LEU* 4.8 3.4 - - - +
41B PHE* 1.3 79.1 - - - +
43B THR* 1.3 58.0 + - - +
44B PHE 3.5 0.2 - - - -
45B PRO* 3.2 22.4 - - - +
46B ILE* 4.2 4.2 + - - +
123B TYR* 4.1 13.6 + - + +
138B ALA* 6.2 3.8 - - + -
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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
------------------------------------------------------------
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