Contacts of the helix formed by residues 14 - 22 (chain D) in PDB entry 3VI4
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 SER 14 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12D ALA 5.2 0.5 - - - -
13D LYS* 1.3 86.0 - - - +
15D CYS* 1.3 63.5 + - - +
16D GLY* 3.5 10.3 + - - -
17D GLU* 3.5 20.7 + - - +
18D CYS* 3.5 19.4 + - - +
27D TRP* 3.9 6.2 + - - -
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Residues in contact with CYS 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D SER* 1.3 74.3 - - - +
16D GLY* 1.3 66.5 + - - +
18D CYS* 3.2 12.3 + - - +
19D ILE* 3.3 11.6 + - - +
27D TRP* 4.0 40.2 - - + +
61D GLU* 3.3 11.0 - - - -
444D CYS* 2.0 53.5 - - + -
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Residues in contact with GLY 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D SER* 3.3 8.1 + - - -
15D CYS* 1.3 80.4 - - - +
17D GLU* 1.3 61.7 + - - +
19D ILE 3.6 0.3 + - - -
20D GLN* 3.0 33.8 + - - +
442D CYS 3.9 15.4 - - - +
443D GLU* 5.4 3.1 - - - -
444D CYS* 4.6 0.9 - - - -
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Residues in contact with GLU 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D ALA* 3.3 34.9 - - + +
13D LYS* 3.4 13.3 + - - +
14D SER* 3.5 21.2 + - - +
16D GLY* 1.3 74.3 - - - +
18D CYS* 1.3 63.4 + - - +
20D GLN* 3.3 7.4 + - - +
21D ALA* 3.2 24.9 + - - +
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Residues in contact with CYS 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D ALA* 5.5 2.0 - - - +
14D SER 3.5 14.1 + - - +
15D CYS* 3.2 11.4 + - - +
16D GLY 3.2 0.8 - - - -
17D GLU* 1.3 80.3 - - - +
19D ILE* 1.3 63.9 + - - +
21D ALA* 3.9 4.3 + - - +
25D CYS* 3.5 17.7 - - - +
26D GLY 3.4 19.1 - - - -
27D TRP* 3.5 18.2 - - + -
44D CYS* 2.0 57.0 - - + -
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Residues in contact with ILE 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D CYS* 3.3 9.0 + - - +
16D GLY 4.2 3.1 - - - +
17D GLU 3.3 0.4 - - - -
18D CYS* 1.3 76.7 - - + +
20D GLN* 1.3 60.3 + - + +
21D ALA 3.1 10.2 + - - -
22D GLY 3.1 17.5 - - - +
25D CYS* 5.2 0.2 - - - -
61D GLU* 5.3 2.0 - - - +
63D PRO* 3.6 24.0 - - + -
104D ARG* 3.2 41.6 + - + +
105D SER* 3.4 6.4 + - - -
441D ILE* 3.9 22.0 - - + +
442D CYS 4.0 5.4 - - - +
443D GLU 3.3 26.2 - - - +
444D CYS* 3.5 19.3 - - - -
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Residues in contact with GLN 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D GLY* 3.0 24.7 + - - +
17D GLU* 3.3 8.9 + - - +
19D ILE* 1.3 74.4 - - - +
21D ALA* 1.3 60.6 + - - +
104D ARG 5.1 1.6 - - - +
105D SER* 4.5 9.7 - - - -
413D ASN* 3.8 10.8 - - - +
414D LYS* 3.7 39.4 + - + +
415D CYS* 3.5 52.1 - - + +
441D ILE 4.7 4.0 - - - +
442D CYS* 4.0 13.2 - - - +
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Residues in contact with ALA 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D ARG* 5.7 5.7 + - - +
7D CYS* 5.6 1.8 - - - -
10D ALA* 4.6 24.7 - - + +
17D GLU 3.2 14.3 + - - +
18D CYS* 4.0 7.9 - - - +
19D ILE 3.1 0.8 + - - -
20D GLN* 1.3 80.6 - - - +
22D GLY* 1.3 59.7 + - - +
23D PRO* 4.8 0.7 - - - +
25D CYS* 4.5 6.1 - - - -
44D CYS* 5.9 0.9 - - - -
105D SER* 4.9 2.7 + - - -
414D LYS* 4.8 9.4 + - - +
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Residues in contact with GLY 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D ARG* 5.7 5.2 - - - -
7D CYS* 3.7 18.1 - - - -
19D ILE 3.1 3.8 + - - +
21D ALA* 1.3 80.8 - - - +
23D PRO* 1.3 66.0 - - - +
24D ASN 3.5 1.3 - - - -
25D CYS* 3.5 9.7 - - - +
104D ARG* 2.8 28.4 + - - -
105D SER* 3.6 6.5 - - - -
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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