Contacts of the helix formed by residues 33 - 49 (chain A) in PDB entry 1VI7
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 33 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A HIS* 4.1 14.7 - - + -
32A THR* 1.3 71.8 - - - +
34A GLY* 1.3 62.1 + - - +
37A ALA* 2.9 18.5 + - - +
61A ALA 4.6 6.1 - - - +
69A GLN* 5.6 0.5 - - - +
97A GLU* 3.8 34.8 - - - +
136A LYS* 4.7 6.4 - - - -
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Residues in contact with GLY 34 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A THR* 3.2 6.4 + - - +
33A ASP* 1.3 79.2 + - - +
35A VAL* 1.3 60.6 + - - -
36A GLU 3.4 2.5 - - - -
37A ALA* 3.2 6.1 - - - +
38A ALA* 3.0 25.0 + - - +
59A TRP* 5.9 0.4 - - - -
61A ALA* 3.8 21.7 - - - +
69A GLN* 4.5 6.5 - - - -
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Residues in contact with VAL 35 (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 GLY* 1.3 70.0 - - - -
36A GLU* 1.3 66.0 + - - +
38A ALA* 3.3 7.0 + - - +
39A LYS* 3.0 27.5 + - + +
59A TRP* 4.1 34.5 - - + +
61A ALA* 5.4 0.2 - - + -
69A GLN* 4.8 20.6 - - + +
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Residues in contact with GLU 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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34A GLY 3.4 1.0 - - - -
35A VAL* 1.3 74.3 - - - +
37A ALA* 1.3 54.0 - - - +
39A LYS* 2.9 10.5 + - + +
40A ALA* 2.5 40.2 + - + +
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Residues in contact with ALA 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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32A THR* 3.6 15.3 - - + +
33A ASP 2.9 41.2 + - - +
34A GLY 3.2 4.0 - - - +
36A GLU* 1.3 77.6 + - - +
38A ALA* 1.3 65.4 + - - +
40A ALA* 3.0 25.1 + - - +
41A PHE* 3.5 3.8 + - - -
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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
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32A THR* 3.6 5.1 - - - +
34A GLY 3.0 12.4 + - - +
35A VAL* 3.5 9.9 - - - +
37A ALA* 1.3 78.4 - - - +
39A LYS* 1.3 61.4 + - - +
40A ALA 3.3 0.2 + - - -
41A PHE* 3.5 9.5 + - - -
42A VAL* 2.9 23.1 + - - +
59A TRP* 3.8 31.9 - - + -
99A THR* 3.2 28.9 - - + +
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Residues in contact with LYS 39 (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 VAL* 3.0 13.3 + - + +
36A GLU* 2.9 12.0 + - + +
38A ALA* 1.3 79.3 - - - +
40A ALA* 1.3 65.7 + - - +
42A VAL* 2.9 49.3 - - + +
43A GLU* 3.6 3.6 + - - +
57A VAL* 6.0 2.4 - - - +
59A TRP* 4.7 20.9 - - - -
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Residues in contact with ALA 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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36A GLU* 2.5 19.9 + - + +
37A ALA* 3.0 21.5 + - - +
39A LYS* 1.3 75.2 - - - +
41A PHE* 1.3 59.3 + - + +
42A VAL 3.4 0.2 + - - -
43A GLU* 3.6 16.6 - - - +
44A SER* 4.0 2.3 + - - -
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Residues in contact with PHE 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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28A MET* 4.1 26.9 - - + -
29A LEU 4.5 1.8 - - - -
30A ALA* 3.8 24.2 - - + -
32A THR* 3.3 24.5 - - + -
37A ALA 3.9 0.7 - - - -
38A ALA 3.6 6.3 - - - -
40A ALA* 1.3 75.7 - - + +
42A VAL* 1.3 65.5 + - + +
43A GLU 3.2 0.9 - - - -
44A SER* 2.9 26.0 + - - +
45A VAL* 3.1 15.5 + - + +
99A THR* 3.2 50.3 - - + -
100A ALA 4.6 0.4 - - - -
101A VAL* 4.7 11.7 - - + -
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Residues in contact with VAL 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 24.0 - - - +
39A LYS* 2.9 42.4 - - + +
41A PHE* 1.3 79.2 - - + +
43A GLU* 1.3 58.9 + - + +
45A VAL* 3.4 2.0 + - - +
46A ARG* 2.9 31.1 + - - +
55A HIS* 6.0 0.7 - - - +
57A VAL* 4.3 29.6 - - + -
59A TRP* 5.6 0.7 - - + -
99A THR* 4.9 2.7 - - + -
101A VAL* 4.4 18.3 - - + +
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Residues in contact with GLU 43 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A LYS 4.4 3.6 - - - +
40A ALA 3.6 12.5 + - - +
42A VAL* 1.3 84.3 - - + +
44A SER* 1.3 54.7 + - - +
46A ARG* 3.1 6.7 + - - +
47A ALA* 2.7 49.6 + - - +
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Residues in contact with SER 44 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A ALA 4.0 2.0 + - - -
41A PHE* 2.9 34.9 + - - +
43A GLU* 1.3 81.7 - - - +
45A VAL* 1.3 55.0 + - - +
47A ALA* 3.6 5.9 - - - +
48A GLU* 2.9 31.6 + - - +
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Residues in contact with VAL 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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28A MET* 4.4 24.2 - - + +
41A PHE* 3.1 17.5 + - + +
42A VAL 3.9 3.1 - - - +
44A SER* 1.3 74.9 + - - +
46A ARG* 1.3 69.6 + - - +
48A GLU* 4.3 7.0 - - - -
49A HIS* 3.1 28.1 + - - +
55A HIS* 4.0 5.1 - - + -
101A VAL* 4.3 26.2 - - + -
103A VAL* 4.5 3.6 - - + -
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Residues in contact with ARG 46 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A VAL 2.9 18.9 + - - +
43A GLU* 3.5 7.2 - - - +
45A VAL* 1.3 74.2 - - - +
47A ALA* 1.3 69.4 + - - +
49A HIS 2.7 24.7 + - - +
50A PRO* 3.4 3.1 - - - +
55A HIS* 4.0 27.1 - - + +
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Residues in contact with ALA 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 GLU* 2.7 36.9 + - - +
44A SER* 3.6 7.4 - - - +
46A ARG* 1.3 74.1 - - - +
48A GLU* 1.3 65.0 + - - +
49A HIS 3.1 0.2 + - - -
50A PRO* 3.4 18.0 - - - +
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Residues in contact with GLU 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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28A MET* 4.3 16.6 - - - +
44A SER 2.9 17.6 + - - +
45A VAL* 4.8 0.7 - - - -
46A ARG 3.0 0.2 + - - -
47A ALA* 1.3 79.5 - - - +
49A HIS* 1.3 94.0 + - + +
50A PRO* 3.6 5.8 - - - +
105A TYR* 4.7 0.9 + - - -
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Residues in contact with HIS 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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26A ILE* 5.1 10.1 - - + -
28A MET* 4.3 11.5 - - - -
45A VAL* 3.1 24.5 + - - +
46A ARG 2.7 12.7 + - - +
48A GLU* 1.3 105.9 + - + +
50A PRO* 1.3 66.1 - - - +
51A ASP 3.3 1.6 - - - -
52A ALA* 3.7 1.5 + - + -
55A HIS* 2.8 23.9 + - - -
103A VAL* 3.8 29.3 - - + +
105A TYR* 2.7 39.0 + + + +
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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
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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