Contacts of the helix formed by residues 42 - 53 (chain A) in PDB entry 1VEG
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 42 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A GLY 5.0 7.6 - - - +
37A VAL* 5.4 1.8 - - - -
41A PHE* 1.3 68.0 - - - +
43A THR* 1.3 59.3 + - - +
44A VAL* 4.3 7.0 - - + +
45A VAL* 2.5 45.8 + - + +
46A ALA 2.8 9.2 + - - -
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Residues in contact with THR 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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33A ILE* 3.7 7.7 - - + +
34A ASN* 6.2 0.3 - - - -
37A VAL* 2.8 33.0 - - - +
41A PHE 3.1 2.8 + - - -
42A ASP* 1.3 68.9 - - - +
44A VAL* 1.3 57.7 + - + +
46A ALA* 2.6 23.8 + - - +
47A GLU* 2.6 48.1 + - - +
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Residues in contact with VAL 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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1A GLY* 6.5 0.7 - - - -
2A SER 5.5 7.2 - - - +
4A GLY* 5.0 16.6 - - - -
42A ASP* 3.1 8.0 - - + +
43A THR* 1.3 79.8 - - + +
45A VAL* 1.3 57.1 + - + +
47A GLU* 3.2 7.9 + - - +
48A ALA* 2.6 43.3 + - + +
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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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41A PHE* 4.2 6.7 - - + -
42A ASP* 2.5 31.9 + - + +
44A VAL* 1.3 79.6 - - + +
46A ALA* 1.3 50.7 + - - +
48A ALA* 3.7 5.8 - - - +
49A ALA* 2.5 38.1 + - - +
64A LEU* 3.4 36.1 - - + -
69A GLY* 5.3 1.6 - - - -
70A SER* 5.1 9.6 - - - +
71A LEU* 4.0 14.7 - - + +
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Residues in contact with ALA 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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33A ILE* 3.7 19.7 - - + +
36A LEU* 3.4 38.8 - - + +
41A PHE* 4.2 4.7 + - + +
42A ASP 2.8 6.7 + - - +
43A THR* 2.6 21.1 + - - +
45A VAL* 1.3 74.3 - - - +
47A GLU* 1.3 54.0 + - - +
49A ALA* 3.4 1.5 - - - +
50A LEU* 2.9 37.2 + - - +
64A LEU* 4.6 1.3 - - - -
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Residues in contact with GLU 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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28A PRO* 4.0 7.0 - - + +
30A GLN* 3.8 10.9 + - - -
33A ILE* 3.3 38.6 - - + +
43A THR* 2.6 47.4 + - - +
44A VAL* 3.7 6.1 - - - +
46A ALA* 1.3 72.4 - - - +
48A ALA* 1.3 61.4 + - - +
50A LEU* 3.7 2.1 + - - +
51A ARG* 3.2 30.2 + - - +
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Residues in contact with ALA 48 (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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44A VAL* 2.6 30.0 + - + +
45A VAL* 3.7 5.6 - - - +
47A GLU* 1.3 70.4 - - - +
49A ALA* 1.3 54.8 - - - +
51A ARG* 3.3 11.4 - - - +
52A VAL* 2.7 40.6 + - + +
71A LEU* 4.6 9.4 - - + -
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Residues in contact with ALA 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 VAL 2.5 23.3 + - - +
46A ALA* 3.4 4.5 - - - +
48A ALA* 1.3 68.6 - - - +
50A LEU* 1.3 60.3 + - - +
51A ARG 2.9 1.3 - - - -
52A VAL* 2.5 33.4 + - - +
53A PHE* 2.9 23.1 + - + -
60A ALA* 3.8 11.9 - - + -
64A LEU* 3.7 26.5 - - + -
71A LEU* 4.3 7.2 - - + +
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Residues in contact with LEU 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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28A PRO* 3.4 25.4 - - + -
32A SER* 3.9 22.0 - - - +
33A ILE* 3.3 33.4 - - + -
36A LEU* 3.9 9.0 - - + -
46A ALA 2.9 19.6 + - - +
49A ALA* 1.3 73.5 - - - +
51A ARG* 1.3 53.9 + - - +
53A PHE* 3.3 1.0 - - - +
54A GLY 2.6 10.3 + - - -
55A GLY* 2.5 61.7 + - - +
56A ASN 3.6 3.4 - - - +
57A VAL* 3.5 29.6 - - + +
60A ALA* 4.3 3.1 - - - +
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Residues in contact with ARG 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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27A SER* 5.4 6.2 + - - +
28A PRO* 4.6 15.0 - - + +
47A GLU* 3.2 20.7 + - - +
48A ALA* 3.3 13.0 - - - +
49A ALA 2.8 0.8 + - - -
50A LEU* 1.3 75.1 - - - +
52A VAL* 1.3 66.8 - - + +
54A GLY* 3.2 16.7 + - - +
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Residues in contact with VAL 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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48A ALA* 2.7 33.9 + - + +
49A ALA* 2.5 15.7 + - - +
51A ARG* 1.3 73.3 - - + +
53A PHE* 1.3 75.4 + - + +
54A GLY 3.0 5.0 + - - -
71A LEU* 4.2 13.0 - - + -
75A LEU* 3.1 44.6 - - + +
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Residues in contact with PHE 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 ALA* 2.9 19.9 + - + +
50A LEU 4.4 0.4 - - - +
52A VAL* 1.3 82.7 - - + +
54A GLY* 1.3 50.1 + - - +
55A GLY 2.5 19.1 + - - -
56A ASN* 3.3 16.1 + - - +
59A LEU* 3.5 38.6 - - + +
60A ALA* 3.4 28.7 - - + +
63A THR* 3.4 42.8 - - + -
64A LEU* 5.6 0.2 - - + -
71A LEU* 4.0 22.2 - - + -
72A PRO* 4.7 4.7 - - + -
75A LEU* 5.8 2.7 - - + -
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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