Contacts of the helix formed by residues 26 - 42 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95G PHE* 3.8 24.0 - - + -
6H CYS* 2.0 54.6 - - + -
11H HIS* 5.8 4.9 - - - -
15H TYR* 5.5 4.2 - - - +
25H GLY* 1.3 75.9 - - - +
27H PHE* 1.3 63.7 + - - +
28H VAL 3.4 2.5 - - - -
29H ASP* 3.4 10.7 + - - +
30H ALA* 3.2 21.8 + - - +
105H HIS* 5.0 3.3 - - + +
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Residues in contact with PHE 27 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92G LEU* 5.8 5.8 - - + +
95G PHE* 4.6 13.1 - - + +
21H VAL* 4.0 28.7 - - + +
24H ASN* 4.1 8.7 - - + -
25H GLY 3.5 0.4 - - - +
26H CYS* 1.3 75.6 - - - +
28H VAL* 1.3 60.9 + - - +
29H ASP 3.1 2.5 - - - -
30H ALA* 3.8 7.0 - - - +
31H LEU* 2.9 32.3 + - - +
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Residues in contact with VAL 28 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24H ASN* 3.4 33.4 + - + +
25H GLY 5.2 1.1 - - - +
26H CYS 3.4 1.0 - - - -
27H PHE* 1.3 78.9 - - - +
29H ASP* 1.3 59.9 + - - +
31H LEU* 4.0 6.3 - - - +
32H ASN* 3.8 13.3 + - - +
149H THR* 4.8 4.2 - - - +
152H ILE* 3.6 21.7 - - + +
153H LYS* 3.6 29.1 + - + +
156H LYS* 5.5 2.0 - - + -
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Residues in contact with ASP 29 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25H GLY 5.4 0.9 + - - +
26H CYS* 3.4 12.0 + - - +
27H PHE 3.1 0.4 - - - -
28H VAL* 1.3 78.6 - - - +
30H ALA* 1.3 64.1 + - - +
31H LEU 3.2 2.1 + - - -
32H ASN* 3.4 7.1 + - - +
33H VAL* 3.4 10.0 + - - +
105H HIS* 3.4 26.2 - - + +
106H LEU* 5.4 1.3 - - - +
109H PRO* 3.3 32.6 - - + +
153H LYS* 4.2 7.9 - - - +
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Residues in contact with ALA 30 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88G MET* 5.3 5.9 - - - +
91G TRP* 4.3 25.1 - - + -
92G LEU* 4.8 20.4 - - + +
95G PHE* 5.4 7.2 - - + -
26H CYS 3.2 13.4 + - - +
27H PHE* 3.3 7.6 + - - +
29H ASP* 1.3 77.7 - - - +
31H LEU* 1.3 64.8 + - - +
32H ASN 3.3 0.2 - - - -
33H VAL* 3.5 20.6 + - - +
34H VAL* 3.8 7.3 + - - +
105H HIS* 6.0 3.1 - - + +
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Residues in contact with LEU 31 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92G LEU* 5.4 16.6 - - + +
27H PHE 2.9 17.8 + - - +
28H VAL* 4.0 6.3 - - - +
29H ASP 3.2 0.4 - - - -
30H ALA* 1.3 79.0 - - - +
32H ASN* 1.3 61.0 + - - +
34H VAL* 3.7 4.0 + - + +
35H PRO* 3.2 22.7 - - + +
148H ILE* 5.1 1.8 - - + +
149H THR* 3.8 18.9 - - + +
152H ILE* 4.0 30.5 - - + -
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Residues in contact with ASN 32 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28H VAL 3.8 9.4 + - - +
29H ASP 3.4 9.8 + - - +
30H ALA 3.3 0.4 - - - -
31H LEU* 1.3 80.5 - - - +
33H VAL* 1.3 61.9 + - - +
34H VAL 3.5 0.2 + - - -
35H PRO* 3.5 15.1 - - - +
36H HIS* 3.8 8.7 + - - +
109H PRO* 4.4 16.6 - - + +
142H TYR* 5.5 0.9 + - - -
149H THR* 3.8 22.6 - - - +
153H LYS* 4.9 8.5 - - - -
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Residues in contact with VAL 33 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88G MET* 3.7 30.5 - - + -
29H ASP 3.4 16.6 - - - +
30H ALA* 3.5 12.3 + - - +
31H LEU 3.3 0.8 - - - -
32H ASN* 1.3 75.0 - - - +
34H VAL* 1.3 65.5 + - - +
36H HIS* 3.2 8.0 + - - +
37H VAL* 3.1 21.4 + - + +
108H MET* 4.6 11.2 - - + +
109H PRO* 4.2 25.6 - - + -
112H MET* 4.8 12.1 - - + -
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Residues in contact with VAL 34 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85G LEU* 5.0 6.5 - - + +
88G MET* 4.5 21.5 - - + +
92G LEU* 5.7 8.3 - - + -
30H ALA 3.8 6.2 + - - +
31H LEU* 3.7 6.8 + - + +
33H VAL* 1.3 77.8 - - - +
35H PRO* 1.3 71.3 - - + +
37H VAL* 3.3 6.1 + - - +
38H PHE* 3.0 28.1 + - - +
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Residues in contact with PRO 35 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31H LEU* 3.2 15.7 - - + +
32H ASN* 3.5 13.0 - - - +
34H VAL* 1.3 99.4 - - + +
36H HIS* 1.3 58.7 + - - +
38H PHE* 3.2 8.5 + - + +
39H LEU 2.9 25.3 + - - -
142H TYR* 3.3 25.0 - - + -
145H LEU* 4.1 44.9 - - + +
146H ALA* 5.2 2.7 - - + +
149H THR* 4.9 1.3 - - + -
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Residues in contact with HIS 36 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32H ASN 3.8 6.8 + - - +
33H VAL 3.2 9.1 + - - +
35H PRO* 1.3 79.6 - - - +
37H VAL* 1.3 63.8 + - - +
39H LEU* 3.3 3.5 + - - +
40H LEU* 3.0 24.1 + - - +
112H MET* 3.7 37.0 - - + +
113H ALA* 4.7 0.7 - - - +
116H ALA* 4.2 5.9 - - + +
142H TYR* 3.4 24.1 - - - +
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Residues in contact with VAL 37 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85G LEU* 5.3 2.2 - - + -
88G MET* 5.3 10.8 - - + -
33H VAL* 3.1 17.0 + - + +
34H VAL* 3.6 11.0 - - - +
35H PRO 3.3 0.2 - - - -
36H HIS* 1.3 77.2 - - - +
38H PHE* 1.3 51.2 + - - +
40H LEU* 3.1 3.2 + - - -
41H PHE* 2.7 75.5 + - + -
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Residues in contact with PHE 38 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85G LEU* 4.4 28.4 - - + +
34H VAL 3.0 14.1 + - - +
35H PRO* 3.5 12.3 - - + +
37H VAL* 1.3 77.6 - - - +
39H LEU* 1.3 65.9 + - + +
41H PHE* 4.1 7.3 - - - +
42H ILE* 3.2 34.6 + - + +
138H ALA* 5.2 15.5 - - + -
141H ILE* 5.5 8.7 - - + -
142H TYR* 6.1 2.7 - + + -
145H LEU* 6.1 5.4 - - + -
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Residues in contact with LEU 39 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35H PRO 2.9 16.4 + - - +
36H HIS* 3.7 5.4 - - - +
37H VAL 3.2 0.2 - - - -
38H PHE* 1.3 81.6 - - + +
40H LEU* 1.3 57.2 + - - +
41H PHE 3.6 0.2 - - - -
42H ILE* 4.4 3.3 - - - +
43H THR* 3.5 20.3 + - - -
116H ALA* 5.0 7.9 - - + +
119H THR* 4.7 6.6 - - - -
123H TYR* 4.4 7.6 - - - -
138H ALA 5.7 2.0 - - - +
139H LEU* 6.4 1.8 - - + -
142H TYR* 3.5 28.7 - - + -
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Residues in contact with LEU 40 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36H HIS 3.0 15.1 + - - +
37H VAL* 3.1 6.0 + - - +
39H LEU* 1.3 80.8 - - - +
41H PHE* 1.3 66.6 + - + +
42H ILE 3.5 0.2 - - - -
43H THR* 4.0 4.7 - - - -
44H PHE* 3.3 44.9 + - + -
115H MET* 5.9 5.8 - - + +
116H ALA* 5.6 5.6 - - - +
119H THR* 5.2 10.3 - - - -
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Residues in contact with PHE 41 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81G CYS* 3.3 48.2 - - + +
84G LEU* 3.7 27.4 - - + -
85G LEU* 3.9 26.9 - - + -
37H VAL* 2.7 52.0 + - + +
38H PHE* 4.0 5.6 - - - +
40H LEU* 1.3 88.5 - - + +
42H ILE* 1.3 62.2 + - - +
44H PHE* 4.6 9.0 - + - -
45H PRO* 3.7 16.6 - - - +
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Residues in contact with ILE 42 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38H PHE* 3.2 31.2 + - + +
39H LEU* 4.8 3.4 - - - +
41H PHE* 1.3 79.1 - - - +
43H THR* 1.3 57.7 + - - +
44H PHE 3.5 0.2 - - - -
45H PRO* 3.2 21.1 - - - +
46H ILE* 4.2 4.7 + - - +
123H TYR* 4.1 13.5 + - + +
138H ALA* 6.2 3.6 - - + -
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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) + - + + + + + -
------------------------------------------------------------
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