Contacts of the helix formed by residues 35 - 47 (chain A) in PDB entry 2UVQ
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 GLY 35 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A ALA 3.2 2.4 - - - -
34A SER* 1.3 74.6 - - - +
36A LYS* 1.3 64.3 + - - +
39A VAL* 2.9 31.8 + - - +
158A VAL* 4.2 5.4 - - - -
213A GLY* 5.0 0.4 - - - -
1236A ADP 2.6 46.5 + - - -
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Residues in contact with LYS 36 (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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28A VAL* 4.0 6.5 - - + +
29A SER 3.4 30.7 - - - +
30A GLY 2.8 26.5 - - - +
31A GLY 3.2 8.9 + - - -
32A THR* 4.0 0.2 - - - +
34A SER* 3.4 8.0 + - - +
35A GLY* 1.3 78.6 - - - +
37A SER* 1.3 65.1 + - - +
39A VAL* 3.6 2.0 - - - +
40A CYS* 2.9 27.6 + - - -
138A GLU* 3.4 25.3 + - + +
139A GLY* 3.9 12.5 - - - +
140A ILE* 3.7 23.6 - - - +
158A VAL* 4.3 8.5 - - + +
1236A ADP 2.6 40.9 + - - +
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Residues in contact with SER 37 (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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36A LYS* 1.3 71.3 - - - +
38A THR* 1.3 58.7 + - - +
40A CYS* 3.3 5.6 + - - +
41A GLU* 2.9 44.7 + - - +
61A ILE* 6.3 0.4 - - - -
65A ASP* 5.7 0.2 + - - -
138A GLU* 3.1 26.7 + - - -
172A ARG* 4.7 3.6 + - - -
1236A ADP 2.8 38.7 + - - -
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Residues in contact with THR 38 (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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35A GLY 3.5 2.9 + - - -
37A SER* 1.3 75.3 - - - +
39A VAL* 1.3 61.4 + - - +
41A GLU* 3.7 9.3 - - - +
42A LYS* 3.0 26.5 + - - +
214A VAL* 2.7 34.5 - - - +
1236A ADP 3.0 60.2 + - - +
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Residues in contact with VAL 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A VAL* 5.5 5.2 - - + -
35A GLY 2.9 26.4 + - - +
36A LYS* 3.6 4.5 - - - +
38A THR* 1.3 73.7 - - - +
40A CYS* 1.3 67.0 + - - +
42A LYS* 3.0 16.9 + - - +
43A ILE* 3.0 30.0 + - + +
156A LEU* 6.5 0.9 - - + -
158A VAL* 4.7 12.1 - - + -
210A ILE* 5.3 12.6 - - + -
213A GLY* 3.5 38.6 - - - +
214A VAL* 3.6 7.2 - - + +
220A ILE* 4.1 14.6 - - + -
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Residues in contact with CYS 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A VAL* 4.0 22.4 - - - -
36A LYS 2.9 17.8 + - - +
37A SER* 3.6 7.6 - - - +
39A VAL* 1.3 77.5 - - - +
41A GLU* 1.3 62.8 + - - +
43A ILE* 3.2 8.6 + - - +
44A MET* 3.0 26.2 + - - +
61A ILE* 3.4 25.1 - - + -
136A LEU* 4.1 21.9 - - + +
138A GLU* 4.0 23.6 - - - -
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Residues in contact with GLU 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A SER* 2.9 35.0 + - - +
38A THR* 3.7 10.3 - - - +
40A CYS* 1.3 76.8 - - - +
42A LYS* 1.3 58.1 + - - +
44A MET* 3.1 5.8 + - - +
45A GLU* 2.8 30.5 + - - +
50A ASN* 4.4 9.0 - - - +
61A ILE* 3.2 28.6 - - + +
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Residues in contact with LYS 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 THR 3.0 14.0 + - - +
39A VAL* 3.0 11.7 + - - +
41A GLU* 1.3 74.9 - - - +
43A ILE* 1.3 52.4 + - - +
45A GLU* 2.9 31.2 + - - +
46A LEU* 2.8 55.8 + - + +
214A VAL* 3.9 15.3 - - + -
217A MET* 3.5 36.6 - - + +
220A ILE* 4.2 19.1 - - + -
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Residues in contact with ILE 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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28A VAL* 6.6 0.2 - - + -
39A VAL* 3.0 33.6 + - + +
40A CYS* 3.6 11.4 - - - +
41A GLU 3.2 0.2 - - - -
42A LYS* 1.3 72.7 - - - +
44A MET* 1.3 60.8 + - - +
46A LEU* 4.1 0.5 - - - +
47A LEU* 3.0 36.8 + - + +
136A LEU* 4.0 18.8 - - + -
156A LEU* 5.8 4.5 - - + -
220A ILE* 3.8 21.3 - - + +
223A ILE* 4.1 24.0 - - + -
224A VAL* 4.1 16.6 - - + -
227A ILE* 3.7 27.6 - - + -
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Residues in contact with MET 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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40A CYS 3.0 17.9 + - - +
41A GLU* 3.5 7.0 - - + +
43A ILE* 1.3 73.6 - - - +
45A GLU* 1.3 65.0 + - - +
47A LEU* 3.5 2.1 + - - -
48A GLY 3.1 2.4 + - - -
49A GLN* 2.9 47.2 + - + +
50A ASN* 3.4 18.3 + - - +
57A ARG* 3.8 27.6 - - - +
59A VAL* 3.1 49.4 - - - +
60A VAL* 4.1 5.6 - - - -
61A ILE* 3.6 29.8 - - + +
136A LEU* 4.5 1.8 - - + -
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Residues in contact with GLU 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 GLU 2.8 14.1 + - - +
42A LYS* 2.9 46.0 + - - +
44A MET* 1.3 76.7 - - - +
46A LEU* 1.3 62.6 + - - +
48A GLY* 3.0 19.1 + - - -
50A ASN* 3.5 22.6 + - + +
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Residues in contact with LEU 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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42A LYS* 2.8 43.4 + - + +
43A ILE 4.1 0.2 - - - +
45A GLU* 1.3 80.4 - - - +
47A LEU* 1.3 60.9 + - - +
48A GLY* 3.1 1.4 + - - -
217A MET* 5.1 2.7 - - - -
220A ILE* 3.6 25.6 - - + -
221A ASN* 3.4 25.1 - - - +
224A VAL* 3.9 23.1 - - + +
228A GLN* 5.2 1.6 - - - +
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Residues in contact with LEU 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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43A ILE* 3.0 35.4 + - + +
44A MET* 4.0 3.8 - - - +
45A GLU 3.3 0.2 - - - -
46A LEU* 1.3 74.4 - - - +
48A GLY* 1.3 59.1 + - - +
49A GLN* 3.2 18.5 + - + +
59A VAL* 3.7 21.5 - - + -
224A VAL* 3.7 17.0 - - + +
227A ILE* 3.3 35.9 - - + -
228A GLN* 3.4 41.0 + - - +
231A LEU* 4.4 5.8 - - + -
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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
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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