Contacts of the helix formed by residues 29 - 38 (chain D) in PDB entry 3VZC
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 29 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25D GLY 2.9 1.6 + - - -
26D GLY 3.2 11.3 + - - +
27D LYS* 3.7 30.8 + - - +
28D GLY* 1.3 84.6 - - - +
30D ALA* 1.3 54.7 + - - +
31D LEU* 3.2 3.4 - - - -
32D GLN* 3.0 45.7 + - + +
33D LEU* 2.7 43.3 + - + +
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Residues in contact with ALA 30 (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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21D LEU* 3.8 13.2 - - + +
22D ASN 3.4 22.7 - - - +
23D PRO* 4.4 1.8 + - + -
25D GLY 2.7 26.1 + - - +
28D GLY 3.7 1.0 - - - -
29D LYS* 1.3 70.4 - - - +
31D LEU* 1.3 53.1 + - - +
33D LEU* 3.3 12.2 + - - +
34D PHE* 2.7 34.3 + - - +
78D MET* 3.6 6.3 - - + +
110D ALA* 3.9 17.5 - - + -
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Residues in contact with LEU 31 (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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21D LEU* 3.9 23.3 - - + +
23D PRO* 4.9 10.3 + - + +
28D GLY 5.5 0.6 + - - +
29D LYS* 3.2 1.3 - - - -
30D ALA* 1.3 78.5 - - - +
32D GLN* 1.3 57.6 + - - +
34D PHE* 3.0 6.2 + - + +
35D ARG* 3.0 58.0 + - + +
51D LEU* 4.1 26.2 - - + -
53D LEU* 4.7 18.6 - - + -
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Residues in contact with GLN 32 (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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29D LYS* 3.0 47.1 + - + +
31D LEU* 1.3 77.9 - - - +
33D LEU* 1.3 69.5 + - + +
35D ARG* 3.2 8.1 + - - +
36D SER* 3.0 31.1 + - - +
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Residues in contact with LEU 33 (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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26D GLY* 4.6 17.3 - - - +
29D LYS* 2.7 32.8 + - + +
30D ALA* 3.6 9.2 - - - +
32D GLN* 1.3 77.6 - - - +
34D PHE* 1.3 61.2 + - - +
36D SER* 3.8 4.0 - - - +
37D HIS* 2.8 48.1 + - + +
38D VAL* 3.7 1.4 + - - +
78D MET* 4.2 4.3 - - + -
110D ALA* 5.0 11.2 - - + +
132D GLU* 3.4 26.5 - - - +
135D LEU* 3.9 20.8 - - + +
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Residues in contact with PHE 34 (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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19D VAL* 4.2 17.3 - - + -
21D LEU* 3.8 14.4 - - + -
30D ALA 2.7 17.3 + - - +
31D LEU* 3.0 9.6 + - + +
33D LEU* 1.3 74.7 - - - +
35D ARG* 1.3 67.2 + - + +
38D VAL* 3.0 39.2 + - + -
39D GLN* 2.8 41.4 + - + -
42D LEU* 4.2 9.0 - - + -
49D PHE* 3.5 52.5 - + - -
51D LEU* 3.9 25.1 - - + -
78D MET* 3.8 16.5 - - - +
108D LEU* 5.4 1.8 - - + -
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Residues in contact with ARG 35 (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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31D LEU* 3.0 50.3 + - + +
32D GLN* 3.2 7.1 + - - +
34D PHE* 1.3 83.2 - - + +
36D SER* 1.3 56.8 + - - +
39D GLN* 3.7 26.5 + - - +
40D PRO* 3.5 17.7 - - - +
51D LEU* 4.2 16.8 - - - +
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Residues in contact with SER 36 (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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32D GLN* 3.0 20.3 + - - +
33D LEU* 3.6 3.5 + - - +
35D ARG* 1.3 79.2 - - - +
37D HIS* 1.3 82.8 + - - +
38D VAL 3.7 0.4 - - - -
40D PRO* 3.6 15.2 - - - +
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Residues in contact with HIS 37 (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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33D LEU* 2.8 31.3 + - + +
36D SER* 1.3 99.0 + - - +
38D VAL* 1.3 61.8 + - - +
40D PRO* 4.3 2.5 - - - -
41D LEU* 3.4 24.1 - - - +
132D GLU* 3.8 29.9 - - + +
135D LEU* 3.8 21.1 - - + -
136D THR* 3.6 23.7 + - - +
139D THR* 4.2 3.8 + - - +
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Residues in contact with VAL 38 (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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33D LEU 4.0 2.5 - - - +
34D PHE* 3.0 42.3 + - + +
37D HIS* 1.3 81.7 - - - +
39D GLN* 1.3 68.7 + - - +
40D PRO* 3.3 2.7 - - - -
41D LEU* 3.1 14.9 + - - +
42D LEU* 3.1 24.3 + - + +
78D MET* 4.0 8.1 - - + -
108D LEU* 3.8 18.2 - - + -
135D LEU* 3.8 20.4 - - + -
139D THR* 3.6 24.5 - - + +
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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