Contacts of the helix formed by residues 37 - 56 (chain B) in PDB entry 4UY1
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 ASP 37 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B TYR* 2.7 34.5 + - - -
35B PRO 3.4 1.2 - - - -
36B ARG* 1.3 78.5 - - - +
38B ALA* 1.3 67.1 + - - +
39B ILE* 3.5 5.0 + - - +
40B ASP* 3.1 18.6 + - - +
41B TRP* 3.0 32.2 + - - -
102B GLU 4.5 2.6 - - - +
104B ASN* 2.8 27.2 + - - +
107B TYR* 3.7 11.7 - - + -
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Residues in contact with ALA 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ASP* 1.3 76.9 - - - +
39B ILE* 1.3 63.9 + - - +
41B TRP* 3.0 13.9 + - - -
42B CYS* 3.0 11.3 + - - -
101B THR* 3.8 23.6 - - + -
102B GLU 5.4 3.8 - - - +
1132B PEG 3.3 39.6 + - - +
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Residues in contact with ILE 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ARG* 4.0 5.8 - - - +
20B TYR* 3.7 25.4 - - + -
23B TYR* 3.6 30.7 - - + +
27B CYS* 3.8 6.3 - - - -
37B ASP* 3.5 2.1 + - - +
38B ALA* 1.3 78.2 - - - +
40B ASP* 1.3 61.0 + - - +
42B CYS* 3.1 14.2 + - - +
43B CYS* 3.1 12.6 + - - -
98B LEU* 3.8 11.4 - - + -
101B THR* 3.3 28.9 - - + +
102B GLU 3.6 17.9 - - - +
103B TYR* 3.5 35.2 - - + -
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Residues in contact with ASP 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B TYR* 3.7 3.9 - - + +
24B GLY* 3.9 7.0 - - - -
25B CYS* 2.8 24.1 + - - +
26B PHE* 2.8 32.3 + - - +
27B CYS* 3.7 10.2 + - - -
35B PRO* 3.4 11.4 - - + +
36B ARG* 2.8 31.2 + - + +
37B ASP* 3.1 22.4 + - - +
39B ILE* 1.3 76.0 - - - +
41B TRP* 1.3 58.0 + - - +
43B CYS* 3.3 1.2 + - - +
44B HIS* 3.0 27.7 + - - +
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Residues in contact with TRP 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B GLN* 3.9 17.7 + - - -
35B PRO* 3.6 31.6 + - + +
37B ASP* 3.0 27.0 + - - -
38B ALA* 3.0 9.8 + - - +
40B ASP* 1.3 74.4 - - - +
42B CYS* 1.3 63.3 + - - +
44B HIS* 3.7 28.7 - + - +
45B GLY* 3.1 19.6 + - - -
97B CYS* 5.0 0.2 - - - -
120B PRO* 3.6 25.8 - - + -
121B LYS 5.7 0.2 - - - -
1132B PEG 3.5 14.6 - - - +
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Residues in contact with CYS 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ALA 3.0 18.9 + - - -
39B ILE 3.1 7.6 + - - +
41B TRP* 1.3 76.4 - - - +
43B CYS* 1.3 57.6 + - - +
45B GLY* 3.5 1.8 + - - -
46B HIS* 3.1 26.9 + - - +
94B ILE* 3.6 10.4 - - + +
97B CYS* 2.1 66.4 - - + -
98B LEU* 3.6 20.2 - - + -
101B THR* 4.0 3.6 - - - -
1132B PEG 3.9 4.9 - - - -
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Residues in contact with CYS 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B TYR* 4.8 5.4 - - - -
26B PHE* 3.8 4.3 - - - -
27B CYS* 2.0 66.2 - - - +
39B ILE* 3.1 10.7 + - - -
40B ASP 3.3 4.7 + - - +
41B TRP 3.3 0.2 - - - -
42B CYS* 1.3 75.4 - - - +
44B HIS* 1.3 59.0 + - - +
46B HIS 3.4 0.2 + - - -
47B ASP* 2.9 28.8 + - - -
94B ILE* 4.2 15.9 - - - -
98B LEU* 4.9 2.5 - - - -
1129B TJM 3.3 22.0 + - - +
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Residues in contact with HIS 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B PHE* 3.5 46.8 - + + +
35B PRO* 4.3 6.7 - - + -
40B ASP 3.0 16.9 + - - +
41B TRP* 3.7 29.5 - + + +
42B CYS 3.4 0.2 - - - -
43B CYS* 1.3 75.9 - - - +
45B GLY* 1.3 64.1 + - - +
47B ASP* 3.2 5.9 + - + +
48B CYS* 3.0 44.0 + - - -
119B SER* 4.6 1.5 - - - -
120B PRO* 2.7 36.5 + - + +
121B LYS 3.3 15.5 - - - -
122B CYS* 4.5 1.7 - - - -
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Residues in contact with GLY 45 (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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41B TRP 3.1 11.7 + - - -
42B CYS 3.8 3.4 - - - -
44B HIS* 1.3 82.4 + - - +
46B HIS* 1.3 56.3 + - - +
48B CYS* 3.2 10.7 + - - +
49B CYS* 3.0 27.1 + - - +
93B GLU* 4.8 6.9 - - - +
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Residues in contact with HIS 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B LEU* 3.7 20.3 - - + +
42B CYS 3.1 17.4 + - - +
43B CYS 3.6 5.6 - - - +
44B HIS 3.3 0.2 - - - -
45B GLY* 1.3 73.5 - - - +
47B ASP* 1.3 55.3 + - - +
49B CYS* 3.1 5.3 + - - +
50B TYR* 2.8 68.6 + + - +
90B CYS* 3.2 28.2 + - + -
91B ASP* 2.8 23.0 + - - -
93B GLU* 5.5 1.3 - - - -
94B ILE* 3.7 21.1 - - + +
1125B 1PE 3.4 9.7 + - - -
1129B TJM 3.2 20.4 + - - +
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Residues in contact with ASP 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B PHE* 3.5 19.7 - - + +
30B GLY 3.1 11.4 - - - +
31B GLY 5.0 0.7 - - - +
43B CYS 2.9 14.4 + - - -
44B HIS* 3.4 11.0 - - + +
46B HIS* 1.3 72.1 - - - +
48B CYS* 1.3 61.0 + - - +
50B TYR* 3.8 1.2 - - - +
51B THR* 2.8 35.9 + - - +
200B CA 2.4 30.7 - - - -
1125B 1PE 2.8 21.9 + - - +
1129B TJM 3.0 9.9 + - - -
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Residues in contact with CYS 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B HIS* 3.0 34.3 + - - -
45B GLY* 3.3 12.3 - - - +
47B ASP* 1.3 77.5 - - - +
49B CYS* 1.3 58.4 + - - +
51B THR* 3.3 5.0 + - - -
52B ARG* 3.1 42.0 + - - +
122B CYS* 2.0 63.7 - - + +
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Residues in contact with CYS 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B GLY 3.0 12.7 + - - +
46B HIS* 3.1 10.7 + - - +
48B CYS* 1.3 75.6 - - - +
50B TYR* 1.3 58.7 + - - +
52B ARG* 3.4 12.9 + - - +
53B ALA* 3.1 23.0 + - - +
86B LEU* 5.7 2.1 - - - +
89B LYS* 4.9 2.2 - - - -
90B CYS* 2.0 62.5 - - + -
93B GLU* 4.2 12.6 - - - +
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Residues in contact with TYR 50 (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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1B GLY 4.5 1.9 + - - -
2B ILE* 6.5 0.2 - - - -
5B LEU* 3.8 13.7 - - + +
46B HIS* 2.8 36.3 + + - +
47B ASP 4.0 2.2 - - - +
49B CYS* 1.3 75.6 - - - +
51B THR* 1.3 63.0 + - - +
53B ALA* 3.4 2.3 + - - -
54B GLU* 3.1 31.0 + - - +
60B PRO* 3.5 47.8 + - + +
61B LYS* 4.2 11.9 - - + -
87B LEU* 4.8 6.7 - - + +
90B CYS* 3.8 17.3 - - + -
91B ASP* 2.6 38.7 + - - -
1125B 1PE 3.4 36.1 - - - +
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Residues in contact with THR 51 (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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47B ASP* 2.8 26.4 + - - +
48B CYS* 3.7 7.1 - - - -
49B CYS 3.3 0.2 - - - -
50B TYR* 1.3 75.7 - - - +
52B ARG* 1.3 58.5 + - - +
54B GLU* 3.3 14.4 + - - +
55B GLU* 3.1 46.6 + - + +
122B CYS* 5.8 3.4 - - - -
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Residues in contact with ARG 52 (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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48B CYS* 3.1 39.5 + - - +
49B CYS* 3.6 10.4 - - - +
51B THR* 1.3 76.4 - - - +
53B ALA* 1.3 60.1 + - - +
55B GLU* 3.3 16.6 + - + +
56B ALA* 3.0 28.8 + - - +
86B LEU* 5.0 1.7 - - + +
122B CYS* 3.3 29.6 + - - +
123B ASP* 3.4 20.7 - - - +
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Residues in contact with ALA 53 (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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49B CYS 3.1 17.1 + - - +
50B TYR* 3.7 8.3 - - - +
51B THR 3.4 0.2 - - - -
52B ARG* 1.3 73.2 - - - +
54B GLU* 1.3 63.8 + - - +
56B ALA 3.4 1.0 + - - -
57B GLY 3.3 4.7 + - - -
58B CYS* 2.8 34.1 + - + +
60B PRO* 4.5 2.5 - - + -
86B LEU* 4.0 26.1 - - + +
87B LEU* 3.8 28.5 - - + -
90B CYS* 5.1 1.3 - - - -
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Residues in contact with GLU 54 (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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50B TYR* 3.1 17.5 + - - +
51B THR* 3.6 14.0 + - + +
52B ARG 3.2 0.2 - - - -
53B ALA* 1.3 76.3 - - - +
55B GLU* 1.3 59.7 + - + +
57B GLY* 3.0 19.9 + - - -
58B CYS 3.5 10.2 + - - +
60B PRO* 3.5 31.4 - - + +
61B LYS* 5.1 7.6 - - - -
1130B PEG 4.0 16.8 - - - +
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Residues in contact with GLU 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B THR* 3.1 39.3 + - + +
52B ARG* 3.6 19.0 - - + +
54B GLU* 1.3 77.0 - - + +
56B ALA* 1.3 57.4 + - - +
57B GLY 3.2 1.2 + - - -
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Residues in contact with ALA 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B ARG 3.0 16.4 + - - +
53B ALA 3.9 5.8 - - - +
54B GLU 3.2 0.6 - - - -
55B GLU* 1.3 75.2 - - - +
57B GLY* 1.3 58.4 + - - +
58B CYS* 3.7 5.6 - - - -
83B CYS* 5.3 0.9 - - - -
86B LEU* 4.3 18.4 - - + -
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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
------------------------------------------------------------
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