Contacts of the helix formed by residues 38 - 45 (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 VAL 38 (chain D).
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Specific contacts
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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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Residues in contact with GLN 39 (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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34D PHE* 2.8 36.1 + - + +
35D ARG* 3.7 32.5 + - - +
38D VAL* 1.3 72.9 - - - +
40D PRO* 1.4 68.6 - - + +
42D LEU* 3.3 8.4 + - - +
43D ALA* 3.2 21.1 + - + +
49D PHE* 3.8 28.6 - - + -
51D LEU* 5.6 0.3 - - - +
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Residues in contact with PRO 40 (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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35D ARG 3.5 18.6 - - - +
36D SER* 3.6 17.0 - - - +
37D HIS 4.9 1.1 - - - -
38D VAL 3.3 10.8 - - - +
39D GLN* 1.4 93.1 - - + +
41D LEU* 1.3 65.3 + - + +
43D ALA* 3.6 14.2 + - + +
44D GLU* 3.6 13.0 + - - +
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Residues in contact with LEU 41 (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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37D HIS 3.4 22.9 - - - +
38D VAL 3.1 7.7 + - - +
40D PRO* 1.3 84.2 - - + +
42D LEU* 1.3 60.0 + - - +
44D GLU* 3.4 10.8 + - + +
45D ALA* 3.2 17.5 + - - +
136D THR* 4.3 24.5 - - + +
139D THR* 3.8 20.9 - - + -
140D LEU* 4.9 14.1 - - + -
143D CYS* 3.6 17.0 - - - -
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Residues in contact with LEU 42 (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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17D VAL* 5.5 1.6 - - + -
19D VAL* 5.2 3.4 - - + -
34D PHE* 4.2 11.7 - - + -
38D VAL* 3.1 35.0 + - + +
39D GLN* 3.5 7.6 - - - +
41D LEU* 1.3 73.7 - - - +
43D ALA* 1.3 63.2 + - - +
45D ALA 3.3 1.6 + - - +
46D GLU 3.1 3.3 + - - -
47D ILE* 2.9 54.1 + - + +
49D PHE* 3.9 31.4 - - + -
76D VAL* 6.3 0.7 - - + -
139D THR* 4.5 2.7 - - + -
142D LEU* 4.0 29.6 - - + -
143D CYS* 4.2 16.4 - - - -
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Residues in contact with ALA 43 (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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39D GLN* 3.2 14.4 + - + +
40D PRO* 3.9 10.5 - - + +
41D LEU 3.4 0.6 - - - -
42D LEU* 1.3 74.2 - - - +
44D GLU* 1.3 63.1 + - - +
46D GLU* 3.2 15.8 + - - +
47D ILE 4.9 2.9 - - - +
49D PHE* 6.1 0.4 - - - -
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Residues in contact with GLU 44 (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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13D ARG* 4.0 6.1 + - - -
40D PRO 3.6 9.4 + - - +
41D LEU* 3.4 12.7 + - + +
42D LEU 3.3 0.6 - - - -
43D ALA* 1.3 78.8 - - - +
45D ALA* 1.3 58.3 + - + +
46D GLU* 3.2 12.8 + - - +
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Residues in contact with ALA 45 (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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13D ARG* 3.8 13.7 - - - +
41D LEU 3.2 16.3 + - - +
42D LEU 3.3 2.2 + - - +
44D GLU* 1.3 75.3 - - + +
46D GLU* 1.3 64.0 + - - +
47D ILE* 3.1 10.3 - - + -
143D CYS* 3.8 30.1 - - + +
145D ARG* 2.8 43.3 + - - +
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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