Contacts of the helix formed by residues 35 - 53 (chain H) in PDB entry 2VIG
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 PRO 35 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34H LEU* 1.4 92.4 - - + +
36H GLU* 1.3 60.4 + - - +
37H THR* 4.1 8.5 - - + +
38H HIS* 3.0 33.6 + - + +
39H GLN* 2.9 25.3 + - - +
96H LEU* 4.8 8.7 - - + -
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Residues in contact with GLU 36 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34H LEU 3.6 1.2 + - - -
35H PRO* 1.3 71.5 - - - +
37H THR* 1.3 59.7 + - + +
39H GLN* 3.3 8.8 + - - +
40H MET* 3.0 28.4 + - - +
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Residues in contact with THR 37 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35H PRO* 3.1 6.8 - - + +
36H GLU* 1.3 78.4 - - + +
38H HIS* 1.3 79.3 + - - +
40H MET* 3.3 8.1 + - - +
41H LEU* 3.0 26.0 + - - +
93H LEU* 6.6 0.2 - - - -
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Residues in contact with HIS 38 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34H LEU* 4.4 5.4 - - + -
35H PRO* 3.0 31.9 + - + +
37H THR* 1.3 100.6 + - - +
39H GLN* 1.3 59.9 + - - +
41H LEU* 3.3 8.5 + - + +
42H LEU* 2.9 29.5 + - - +
93H LEU* 6.0 4.0 - - + -
94H ASP* 3.1 35.3 + - - -
96H LEU* 3.9 13.9 - - + +
97H ALA* 3.5 22.5 + - + +
100H ILE* 3.6 32.9 - - + +
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Residues in contact with GLN 39 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34H LEU* 4.5 15.3 - - + +
35H PRO 2.9 12.3 + - - +
36H GLU* 3.6 12.6 - - - +
38H HIS* 1.3 77.4 - - - +
40H MET* 1.3 58.8 + - - +
42H LEU* 3.6 10.3 + - - +
43H GLN* 3.4 20.3 + - - +
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Residues in contact with MET 40 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36H GLU 3.0 13.4 + - - +
37H THR* 3.6 10.5 - - - +
38H HIS 3.3 0.2 - - - -
39H GLN* 1.3 73.0 - - - +
41H LEU* 1.3 67.2 + - - +
43H GLN* 3.3 7.3 + - - +
44H THR* 3.1 25.5 + - - -
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Residues in contact with LEU 41 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37H THR 3.0 14.0 + - - +
38H HIS* 3.3 12.1 + - + +
40H MET* 1.3 77.0 - - - +
42H LEU* 1.3 63.9 + - - +
44H THR* 3.2 9.4 + - + -
45H CYS* 3.0 39.6 + - - -
79H LEU* 4.9 4.7 - - + -
82H MET* 4.0 16.2 - - + -
93H LEU* 4.3 11.2 - - + -
97H ALA* 3.3 48.9 - - + +
100H ILE* 4.5 9.6 - - + -
101H ALA* 4.6 0.4 - - + -
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Residues in contact with LEU 42 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34H LEU* 4.7 14.6 - - + -
38H HIS 2.9 16.7 + - - +
39H GLN* 3.7 10.1 - - - +
41H LEU* 1.3 77.2 - - - +
43H GLN* 1.3 68.5 + - - +
45H CYS* 3.4 2.8 + - - +
46H ARG* 2.9 46.8 + - - +
100H ILE* 3.8 24.7 - - + -
104H GLU* 3.8 24.5 - - + +
329H TRP* 6.1 2.5 - - + -
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Residues in contact with GLN 43 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39H GLN 3.4 10.0 + - - +
40H MET* 3.3 11.1 + - - +
41H LEU 3.2 1.0 - - - -
42H LEU* 1.3 87.1 - - + +
44H THR* 1.3 60.0 + - - +
46H ARG* 4.3 16.6 - - - +
47H ASP* 2.8 65.8 + - - +
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Residues in contact with THR 44 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40H MET 3.1 15.0 + - - -
41H LEU* 3.2 11.8 + - + -
43H GLN* 1.3 75.2 - - - +
45H CYS* 1.3 62.5 + - - +
47H ASP* 3.4 7.6 + - - +
48H PHE* 2.9 28.9 + - + +
77H LEU* 4.8 24.7 - - + -
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Residues in contact with CYS 45 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41H LEU* 3.0 32.3 + - - +
42H LEU* 3.7 2.9 - - - +
44H THR* 1.3 76.0 - - - +
46H ARG* 1.3 61.8 + - - +
48H PHE* 3.3 6.3 + - - +
49H ALA* 2.8 31.4 + - - +
79H LEU* 4.0 17.9 - - - -
101H ALA* 3.6 32.8 - - - +
104H GLU* 3.5 24.3 - - + +
105H ILE* 4.6 7.8 - - + +
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Residues in contact with ARG 46 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42H LEU* 2.9 32.1 + - - +
43H GLN* 3.8 20.6 - - - +
45H CYS* 1.3 76.6 - - - +
47H ASP* 1.3 58.0 + - - +
49H ALA* 3.2 4.4 + - - +
50H GLU* 2.8 35.4 + - + +
103H GLU* 5.7 1.0 + - - -
104H GLU* 3.3 39.3 + - - +
107H ARG* 3.5 41.7 + - - +
284H GLN* 5.4 5.5 - - - +
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Residues in contact with ASP 47 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43H GLN* 2.8 56.2 + - - +
44H THR* 3.7 7.3 + - - +
46H ARG* 1.3 73.1 - - - +
48H PHE* 1.3 57.1 + - - +
50H GLU* 3.4 5.5 + - - +
51H LYS* 3.0 32.3 + - - +
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Residues in contact with PHE 48 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44H THR* 2.9 19.6 + - + +
45H CYS* 3.6 6.7 - - - +
47H ASP* 1.3 76.5 - - - +
49H ALA* 1.3 55.6 + - - +
51H LYS* 4.7 3.1 - - - -
52H GLU* 2.7 63.4 + - + +
53H LEU* 4.0 16.2 - - + -
70H GLN* 3.9 13.2 - - - -
73H LYS* 3.9 19.3 - - + -
74H MET* 3.3 37.9 - - + -
77H LEU* 3.7 26.2 - - + -
79H LEU* 4.8 2.2 - - + -
105H ILE* 3.8 16.4 - - + -
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Residues in contact with ALA 49 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45H CYS 2.8 18.9 + - - +
46H ARG* 3.8 5.2 - - - +
48H PHE* 1.3 73.4 - - - +
50H GLU* 1.3 61.6 + - - +
53H LEU* 3.0 27.1 + - + -
54H PHE* 2.9 36.3 + - + -
104H GLU* 3.4 25.8 - - - +
105H ILE* 4.6 0.7 - - + -
107H ARG* 5.7 0.9 - - - +
108H GLY* 4.2 10.5 - - - -
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Residues in contact with GLU 50 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46H ARG* 2.8 24.4 + - + +
47H ASP* 3.8 6.5 - - - +
49H ALA* 1.3 75.1 - - - +
51H LYS* 1.3 60.0 + - - +
54H PHE* 3.7 19.0 - - + +
55H PRO* 3.8 14.4 - - - +
107H ARG* 6.0 1.1 - - - +
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Residues in contact with LYS 51 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47H ASP 3.0 18.0 + - - +
48H PHE* 3.9 2.7 - - - +
50H GLU* 1.3 78.5 - - - +
52H GLU* 1.3 81.7 + - + +
53H LEU 3.8 0.2 - - - -
55H PRO* 3.5 16.1 - - - +
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Residues in contact with GLU 52 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48H PHE* 2.7 58.0 + - + +
51H LYS* 1.3 105.2 + - + +
53H LEU* 1.3 59.0 + - + +
55H PRO* 3.8 3.5 - - - +
56H ILE* 3.6 22.5 - - - +
70H GLN* 3.7 25.4 + - + +
73H LYS* 3.2 35.2 + - - +
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Residues in contact with LEU 53 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48H PHE* 4.0 12.1 - - + -
49H ALA* 3.0 20.8 + - + +
52H GLU* 1.3 83.7 - - - +
54H PHE* 1.3 69.5 + - - +
55H PRO* 3.3 1.8 - - - -
56H ILE* 3.1 10.8 + - + +
57H ALA* 3.0 23.6 + - - +
70H GLN* 4.1 20.2 - - + -
105H ILE* 3.7 53.6 - - + +
108H GLY 3.8 16.5 - - - +
109H CYS* 4.1 3.0 - - + +
112H THR* 3.8 26.0 - - + +
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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
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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