Contacts of the helix formed by residues 37 - 56 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A TYR* 2.7 31.0 + - - -
35A PRO 3.3 2.0 + - - -
36A ARG* 1.3 79.8 - - - +
38A ALA* 1.3 59.5 + - - +
39A ILE* 3.4 7.0 + - - +
40A ASP* 3.1 23.4 + - - +
41A TRP* 2.9 36.1 + - - -
102A GLU 4.7 1.0 - - - +
104A ASN* 2.8 27.6 + - - +
107A TYR* 3.4 11.5 - - + -
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Residues in contact with ALA 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ASP* 1.3 72.4 - - - +
39A ILE* 1.3 67.0 + - - +
41A TRP* 3.0 13.7 + - - +
42A CYS* 2.9 27.7 + - - -
101A THR* 3.8 21.8 - - + -
102A GLU 5.9 1.1 - - - +
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Residues in contact with ILE 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ARG* 4.2 4.3 - - - +
20A TYR* 3.9 10.1 - - + -
23A TYR* 3.3 42.8 - - + +
27A CYS* 3.8 8.1 - - - -
37A ASP* 3.4 3.4 + - - +
38A ALA* 1.3 78.3 - - - +
40A ASP* 1.3 60.3 + - - +
42A CYS* 3.2 7.7 + - - +
43A CYS* 3.1 20.8 + - - -
98A LEU* 3.8 22.9 - - + -
101A THR* 3.1 25.6 - - - +
102A GLU 3.3 23.5 + - - +
103A TYR* 3.6 24.5 - - + -
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Residues in contact with ASP 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A TYR* 3.5 8.7 - - + +
24A GLY* 3.6 7.9 - - - -
25A CYS* 2.8 26.3 + - - +
26A PHE* 2.9 28.7 + - - +
27A CYS* 3.6 6.1 + - - -
35A PRO* 3.4 11.0 - - + +
36A ARG* 2.9 27.4 + - + +
37A ASP* 3.1 22.8 + - - +
39A ILE* 1.3 73.7 - - - +
41A TRP* 1.3 61.4 + - - +
43A CYS* 3.4 1.0 + - - +
44A HIS* 3.0 27.2 + - - +
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Residues in contact with TRP 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A GLN* 3.9 18.2 - - - +
35A PRO* 3.7 32.1 + - + +
37A ASP* 2.9 28.7 + - - -
38A ALA* 3.0 12.5 + - - +
40A ASP* 1.3 73.4 - - - +
42A CYS* 1.3 64.8 + - - +
44A HIS* 3.2 26.3 + + - +
45A GLY* 3.0 21.8 + - - -
97A CYS* 5.1 0.4 - - - -
120A PRO* 3.7 27.1 - - + -
121A LYS 5.8 0.2 - - - -
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Residues in contact with CYS 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ALA* 2.9 21.0 + - - -
39A ILE 3.2 8.5 + - - +
41A TRP* 1.3 72.3 - - - +
43A CYS* 1.3 57.6 + - - +
45A GLY* 3.5 2.2 + - - -
46A HIS* 3.0 27.0 + - - +
94A ILE* 3.7 8.5 - - + +
97A CYS* 2.0 66.6 - - + -
98A LEU* 3.6 22.0 - - + -
101A THR* 4.2 7.4 - - - -
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Residues in contact with CYS 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A TYR* 5.1 4.5 - - - -
26A PHE* 3.9 2.2 - - - -
27A CYS* 2.0 64.6 - - - +
39A ILE* 3.1 7.8 + - - -
40A ASP 3.7 4.7 - - - +
41A TRP 3.2 0.2 - - - -
42A CYS* 1.3 76.7 - - - +
44A HIS* 1.3 60.2 + - - +
46A HIS* 4.3 1.1 - - - -
47A ASP* 2.9 37.1 + - - +
94A ILE* 4.4 11.4 - - - -
98A LEU* 4.8 3.8 - - - -
1130A TJM 3.5 20.2 + - - +
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Residues in contact with HIS 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A PHE* 3.7 46.0 - + + +
35A PRO* 4.5 3.8 - - + -
40A ASP 3.0 14.8 + - - +
41A TRP* 3.2 26.4 + + - +
43A CYS* 1.3 75.5 - - - +
45A GLY* 1.3 63.9 + - - +
47A ASP* 3.3 6.0 + - + +
48A CYS* 3.0 46.6 + - - -
119A SER* 5.0 0.9 - - - -
120A PRO* 2.9 34.5 + - + +
121A LYS 3.4 22.2 - - - -
122A CYS* 4.4 1.4 - - - -
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Residues in contact with GLY 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A TRP 3.0 13.4 + - - -
42A CYS 3.8 4.5 - - - -
44A HIS* 1.3 82.2 + - - +
46A HIS* 1.3 55.5 + - - +
48A CYS* 3.3 8.2 + - - +
49A CYS* 3.0 27.4 + - - +
52A ARG* 5.0 1.2 + - - -
93A GLU* 4.7 8.5 - - - +
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Residues in contact with HIS 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A LEU* 3.6 22.7 - - + -
42A CYS 3.0 17.3 + - - +
43A CYS 3.8 0.2 - - - +
45A GLY* 1.3 72.4 - - - +
47A ASP* 1.3 60.3 + - - +
49A CYS* 3.2 4.9 + - - +
50A TYR* 2.9 65.1 + + - +
90A CYS* 3.3 27.4 - - + -
91A ASP* 2.8 23.9 + - - -
93A GLU* 5.5 1.3 - - - -
94A ILE* 3.4 25.5 - - + +
1125A 1PE 4.8 1.0 + - - -
1130A TJM 3.1 26.2 + + - +
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Residues in contact with ASP 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A PHE* 3.6 19.5 - - + +
30A GLY 3.3 9.7 - - - +
31A GLY* 4.7 0.5 - - - +
43A CYS 2.9 16.0 + - - -
44A HIS* 3.3 11.0 - - + +
46A HIS* 1.3 76.6 - - - +
48A CYS* 1.3 53.2 + - - +
50A TYR* 4.8 0.2 - - - -
51A THR* 2.8 36.8 + - - -
122A CYS* 5.3 0.2 - - - -
200A CA 2.5 30.3 - - - -
1125A 1PE 3.2 11.4 + - - -
1129A DMS 3.1 14.5 - - + +
1130A TJM 2.9 20.3 + - - +
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Residues in contact with CYS 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A HIS* 3.0 40.0 + - - -
45A GLY* 3.4 11.2 - - - +
46A HIS 3.2 0.2 - - - -
47A ASP* 1.3 73.6 - - - +
49A CYS* 1.3 60.3 + - - +
51A THR* 3.3 5.5 + - - -
52A ARG* 2.9 40.6 + - - +
122A CYS* 2.0 62.0 - - + +
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Residues in contact with CYS 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A GLY 3.0 14.8 + - - +
46A HIS* 3.2 10.7 + - - +
48A CYS* 1.3 75.5 - - - +
50A TYR* 1.3 50.3 + - - +
52A ARG* 3.1 35.7 + - - +
53A ALA* 2.8 33.8 + - - +
89A LYS* 5.0 1.6 - - - -
90A CYS* 2.0 57.1 - - + -
93A GLU* 4.1 11.7 - - - +
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Residues in contact with TYR 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A GLY 4.3 3.1 + - - -
2A ILE* 4.8 2.0 - - + -
5A LEU* 4.0 10.4 - - + +
46A HIS* 2.9 36.7 + + - +
49A CYS* 1.3 77.1 - - - +
51A THR* 1.3 56.3 + - - +
53A ALA* 3.3 5.4 + - + +
54A GLU* 2.9 32.9 + - - +
60A PRO* 3.5 45.3 + - + +
61A LYS* 4.2 9.2 - - + -
87A LEU* 4.9 4.7 - - + -
90A CYS* 3.9 16.6 - - + -
91A ASP* 2.7 36.8 + - - -
1125A 1PE 3.8 32.1 - - - -
1129A DMS 3.6 21.5 - - + +
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Residues in contact with THR 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A ASP* 2.8 22.3 + - - +
48A CYS* 3.5 9.4 - - - +
49A CYS 3.2 0.2 - - - -
50A TYR* 1.3 73.2 - - - +
52A ARG* 1.3 66.1 + - + +
54A GLU* 3.2 13.7 + - - +
55A GLU* 3.0 44.8 + - + +
122A CYS* 5.6 4.7 - - - -
1129A DMS 3.4 17.8 - - + +
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Residues in contact with ARG 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A GLY 5.0 1.4 + - - -
48A CYS* 2.9 21.6 + - - +
49A CYS* 3.1 43.5 + - - +
51A THR* 1.3 77.6 - - + +
53A ALA* 1.3 62.5 + - - +
55A GLU* 3.1 17.8 + - - +
56A ALA* 3.0 23.1 + - - +
86A LEU* 5.9 0.2 - - - -
93A GLU* 5.3 3.6 + - - -
122A CYS* 5.7 6.1 - - + -
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Residues in contact with ALA 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A CYS 2.8 16.9 + - - +
50A TYR* 3.6 11.7 - - - +
51A THR 3.3 0.2 - - - -
52A ARG* 1.3 72.0 - - - +
54A GLU* 1.3 62.9 + - - +
56A ALA* 3.3 12.9 + - - +
57A GLY 3.4 0.7 + - - -
58A CYS* 3.0 28.1 + - + +
60A PRO* 4.4 5.6 - - + -
86A LEU* 4.7 11.4 - - + -
87A LEU* 3.9 27.8 - - + -
90A CYS* 4.9 7.0 - - - -
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Residues in contact with GLU 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A TYR 2.9 15.7 + - - +
51A THR* 3.2 8.0 + - - +
53A ALA* 1.3 77.0 - - - +
55A GLU* 1.3 62.2 + - + +
57A GLY* 3.1 14.2 + - - -
58A CYS 3.6 11.3 + - - +
60A PRO* 3.6 20.5 - - + +
61A LYS* 4.7 0.9 - - - -
1125A 1PE 4.4 2.1 + - - -
1128A DMS 3.4 26.9 - - + +
1129A DMS 2.7 44.0 + - - +
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Residues in contact with GLU 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A THR* 3.0 31.0 + - + +
52A ARG* 3.1 21.7 + - - +
54A GLU* 1.3 77.2 - - + +
56A ALA* 1.3 59.0 + - - +
57A GLY 3.2 1.4 + - - -
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Residues in contact with ALA 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A ARG 3.0 12.0 + - - +
53A ALA 3.6 9.2 - - - +
54A GLU 3.2 0.6 - - - -
55A GLU* 1.3 76.5 - - - +
57A GLY* 1.3 56.3 + - - +
58A CYS* 4.4 4.7 - - - -
83A CYS* 5.3 0.7 - - - -
86A LEU* 4.1 23.8 - - + -
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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
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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