Contacts of the helix formed by residues 33 - 54 (chain G) in PDB entry 6V3O
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 LYS 33 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30G GLU 5.8 0.9 - - - -
31G ASP* 3.3 19.1 + - - +
32G ASP* 1.3 78.5 - - - +
34G LEU* 1.3 59.7 + - - +
35G ILE* 3.2 4.7 - - - -
36G GLU* 3.0 29.4 + - - +
37G TYR* 2.8 49.8 + - + +
116G GLN* 3.7 4.0 - - - +
201G ASN* 2.7 31.6 + - - +
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Residues in contact with LEU 34 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32G ASP* 3.1 7.4 + - - +
33G LYS* 1.3 77.4 - - - +
35G ILE* 1.3 57.4 + - - +
37G TYR* 3.2 6.8 + - + -
38G ASP* 2.9 40.0 + - - +
109G ALA 4.8 0.4 - - - +
112G ALA* 3.7 11.0 - - + +
113G GLU* 3.7 45.3 - - + +
116G GLN* 3.5 25.1 - - + +
889G GLN* 4.1 17.0 - - - +
890G GLY* 4.6 9.0 - - - -
893G LEU* 3.6 27.8 - - + -
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Residues in contact with ILE 35 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17G ASP* 4.6 4.9 - - - +
20G LEU* 3.4 53.5 - - + +
21G ARG* 3.4 45.8 - - - +
24G VAL* 4.2 15.7 - - + -
32G ASP* 4.6 5.2 + - - +
33G LYS* 5.1 2.9 - - - -
34G LEU* 1.3 78.5 - - - +
36G GLU* 1.3 63.1 + - + +
38G ASP* 3.9 4.6 - - - +
39G ALA* 3.0 29.6 + - - +
893G LEU* 4.9 9.8 - - + +
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Residues in contact with GLU 36 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21G ARG* 5.4 6.7 - - - +
33G LYS* 3.0 37.8 + - + +
35G ILE* 1.3 83.3 - - + +
37G TYR* 1.3 63.6 - - + +
39G ALA* 3.4 6.4 + - + +
40G LEU* 2.9 38.1 + - + +
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Residues in contact with TYR 37 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33G LYS* 2.8 32.9 + - + +
34G LEU* 3.4 13.2 - - - +
36G GLU* 1.3 80.3 - - + +
38G ASP* 1.3 64.3 + - - +
40G LEU* 3.1 6.9 + - + +
41G LEU* 2.9 29.0 + - - +
112G ALA* 3.8 28.7 - - + -
115G VAL* 3.9 24.3 - - + +
116G GLN* 4.2 19.1 - - + -
119G HIS* 5.9 2.8 - - - +
197G LEU* 4.0 30.1 + - + -
198G THR* 5.4 1.2 - - - -
201G ASN* 3.7 37.1 + - + +
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Residues in contact with ASP 38 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20G LEU* 3.6 23.2 - - + +
34G LEU* 2.9 26.8 + - - +
35G ILE* 3.9 1.1 - - - +
37G TYR* 1.3 72.8 - - - +
39G ALA* 1.3 64.6 + - - +
41G LEU* 3.2 4.1 + - - +
42G VAL* 3.0 31.3 + - - +
109G ALA* 3.6 26.6 - - - +
112G ALA* 3.2 22.4 - - - +
893G LEU* 3.9 28.1 - - - +
897G TYR* 4.7 6.0 + - - +
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Residues in contact with ALA 39 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15G SER* 4.4 0.4 - - - +
16G ILE* 4.7 9.2 - - - -
17G ASP* 4.1 28.9 - - + +
20G LEU* 4.3 2.4 - - + +
35G ILE 3.0 20.5 + - - +
36G GLU* 3.6 6.5 - - + +
38G ASP* 1.3 75.3 - - - +
40G LEU* 1.3 59.5 + - - +
43G ASP* 2.8 47.6 + - - +
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Residues in contact with LEU 40 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36G GLU* 2.9 23.3 + - + +
37G TYR* 3.6 5.6 - - + +
39G ALA* 1.3 76.4 - - - +
41G LEU* 1.3 64.0 + - - +
43G ASP* 4.2 3.4 - - - +
44G ARG* 3.1 52.5 + - + +
197G LEU* 3.8 19.1 - - + -
200G LEU* 4.5 14.4 - - + -
214G ASP* 5.6 0.9 - - - +
217G LEU* 3.4 32.8 - - + -
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Residues in contact with LEU 41 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37G TYR 2.9 16.8 + - - +
38G ASP* 3.7 4.3 - - - +
40G LEU* 1.3 79.2 - - - +
42G VAL* 1.3 60.1 + - + +
44G ARG* 3.3 4.2 + - - +
45G PHE* 3.0 24.6 + - - +
108G LEU* 3.1 49.8 - - + +
111G LEU* 5.2 1.1 - - + -
112G ALA* 3.7 21.8 - - + +
193G ILE* 4.2 15.3 - - + -
197G LEU* 4.1 26.0 - - + -
217G LEU* 4.2 24.2 - - + -
221G ILE* 3.8 12.8 - - + +
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Residues in contact with VAL 42 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16G ILE* 4.3 14.6 - - + -
38G ASP* 3.0 20.6 + - + +
39G ALA 4.5 0.4 - - - +
41G LEU* 1.3 80.3 - - + +
43G ASP* 1.3 62.5 + - - +
45G PHE* 3.5 5.5 - - + +
46G LEU* 2.9 37.1 + - + +
65G TYR* 6.3 0.2 - - + -
105G MET* 3.5 54.3 - - + +
108G LEU* 4.6 5.4 - - + -
109G ALA 5.4 2.0 - - - +
897G TYR* 3.8 21.8 - - + +
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Residues in contact with ASP 43 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14G HIS 4.6 1.4 - - - +
15G SER* 2.5 32.0 + - - -
16G ILE* 3.1 29.0 + - - +
39G ALA* 2.8 31.1 + - - +
40G LEU* 4.2 3.4 - - - +
42G VAL* 1.3 76.1 - - - +
44G ARG* 1.3 69.6 + - - +
46G LEU* 3.6 6.4 + - - +
47G ASN* 3.2 33.3 + - - +
58G ARG* 4.8 5.1 + - - +
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Residues in contact with ARG 44 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40G LEU* 3.1 45.7 + - + +
41G LEU* 3.5 9.0 - - - +
42G VAL 3.2 0.6 - - - -
43G ASP* 1.3 85.4 - - - +
45G PHE* 1.3 62.6 + - - +
47G ASN* 3.4 14.5 + - - +
48G ILE* 3.1 29.3 + - + +
214G ASP* 2.8 39.6 + - - +
217G LEU* 5.0 4.5 - - + +
218G GLN* 3.7 30.2 - - + +
221G ILE* 4.1 13.7 - - + -
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Residues in contact with PHE 45 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41G LEU 3.0 14.9 + - - +
42G VAL* 3.1 8.2 + - + +
44G ARG* 1.3 78.1 - - - +
46G LEU* 1.3 65.5 + - + +
48G ILE* 3.2 8.2 + - + +
49G LEU* 2.9 34.8 + - + +
101G SER* 3.7 39.3 - - - -
104G HIS* 3.9 12.1 - - + -
105G MET* 3.6 19.3 - - + -
108G LEU* 3.8 18.8 - - + -
221G ILE* 3.8 25.8 - - + +
225G PHE* 3.3 45.8 - + + -
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Residues in contact with LEU 46 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16G ILE* 4.1 17.7 - - + -
42G VAL* 2.9 34.8 + - + +
43G ASP* 4.2 2.7 - - - +
45G PHE* 1.3 79.9 - - + +
47G ASN* 1.3 57.2 + - - +
49G LEU* 3.3 17.8 - - + +
50G GLN* 2.7 31.5 + - - +
58G ARG* 3.4 36.9 - - + +
61G VAL* 4.0 28.3 - - + -
62G GLN* 3.9 23.3 - - + +
105G MET* 4.1 11.2 - - + -
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Residues in contact with ASN 47 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43G ASP* 3.2 22.6 + - - +
44G ARG* 3.7 17.5 - - - +
45G PHE 3.3 0.2 - - - -
46G LEU* 1.3 73.9 - - - +
48G ILE* 1.3 60.6 + - + +
50G GLN* 3.3 5.2 + - - +
51G ASP* 2.8 30.0 + - - +
58G ARG* 2.9 27.7 + - - +
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Residues in contact with ILE 48 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44G ARG 3.1 17.8 + - - +
45G PHE* 3.5 7.6 - - + +
47G ASN* 1.3 74.4 - - + +
49G LEU* 1.3 63.7 + - - +
51G ASP* 3.1 7.8 + - + +
52G LEU* 2.9 50.2 + - + +
218G GLN* 3.3 40.8 - - + +
221G ILE* 3.7 25.6 - - + -
222G GLN* 3.9 28.0 - - + +
225G PHE* 5.7 5.2 - - + -
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Residues in contact with LEU 49 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45G PHE* 2.9 21.9 + - + +
46G LEU* 3.1 27.1 + - + +
48G ILE* 1.3 77.4 - - - +
50G GLN* 1.3 56.9 + - - +
52G LEU* 3.2 3.8 + - - -
53G HIS* 2.9 44.3 + - + +
54G GLY 3.8 1.3 + - - +
57G LEU* 4.6 5.4 - - + +
58G ARG* 4.2 15.0 - - - +
61G VAL* 4.0 28.9 - - + -
97G LEU* 4.5 5.2 - - + -
101G SER* 3.9 19.7 - - - +
225G PHE* 4.0 25.8 - - + -
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Residues in contact with GLN 50 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13G HIS* 3.5 31.9 + - - -
46G LEU 2.7 18.1 + - - +
47G ASN* 3.7 6.6 + - - +
49G LEU* 1.3 73.3 - - - +
51G ASP* 1.3 62.7 + - - +
54G GLY* 3.0 27.6 + - - -
55G PRO* 3.7 26.7 - - + +
58G ARG* 2.8 37.0 - - + +
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Residues in contact with ASP 51 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47G ASN 2.8 21.2 + - - +
48G ILE* 3.1 10.6 + - - +
50G GLN* 1.3 73.0 - - - +
52G LEU* 1.3 70.3 + - + +
54G GLY 5.1 0.2 + - - -
222G GLN* 5.4 3.5 + - - +
427H GLY 5.4 1.4 - - - +
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Residues in contact with LEU 52 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48G ILE* 2.9 38.7 + - + +
49G LEU* 5.1 1.1 - - - +
51G ASP* 1.3 88.8 - - + +
53G HIS* 1.3 78.0 + - + +
54G GLY 3.8 0.2 - - - -
222G GLN* 4.0 13.9 - - + +
225G PHE* 4.4 11.9 - - + -
226G ARG* 3.7 38.0 + - - +
927G LYS 4.7 5.2 - - - +
426H CYS 5.5 0.2 - - - +
427H GLY* 3.5 29.2 - - - +
428H ASP* 4.6 0.9 - - - +
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Residues in contact with HIS 53 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49G LEU* 2.9 23.2 + - + +
52G LEU* 1.3 90.4 + - + +
54G GLY* 1.3 63.2 + - - +
57G LEU* 4.1 14.5 - - + +
97G LEU* 3.3 36.3 - - + +
225G PHE* 4.0 15.8 - + - -
226G ARG* 4.1 16.5 + - - -
925G LEU 3.8 3.3 - - - +
926G SER* 3.4 26.7 + - - -
927G LYS* 3.2 30.0 + - - +
334H ARG* 5.4 1.7 + - - -
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Residues in contact with GLY 54 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49G LEU 3.8 0.5 + - - +
50G GLN* 3.0 23.1 + - - -
51G ASP 4.8 0.2 - - - -
52G LEU 3.8 0.4 - - - -
53G HIS* 1.3 82.0 - - - +
55G PRO* 1.3 76.0 - - - +
56G SER* 3.3 3.5 + - - -
57G LEU* 3.4 2.3 + - - +
58G ARG 3.2 15.9 + - - -
925G LEU 5.4 0.2 - - - -
927G LYS* 5.1 9.9 - - - -
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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