Contacts of the helix formed by residues 29 - 38 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25B GLY 3.0 1.8 + - - -
26B GLY 3.2 15.9 - - - +
27B LYS 4.8 3.1 - - - +
28B GLY* 1.3 82.4 - - - +
30B ALA* 1.3 67.4 + - - +
31B LEU 3.0 4.0 + - - -
32B GLN* 3.0 52.7 + - + +
33B LEU* 2.9 42.1 + - + +
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Residues in contact with ALA 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B LEU* 3.8 13.6 - - + +
22B ASN 3.3 26.0 - - - +
23B PRO 4.1 1.4 + - - +
25B GLY 2.9 12.1 + - - +
28B GLY 3.8 0.6 - - - -
29B LYS* 1.3 77.8 - - - +
31B LEU* 1.3 57.6 + - - +
33B LEU* 3.4 5.5 + - - +
34B PHE* 2.8 25.5 + - - +
78B MET* 3.3 11.8 - - + +
110B ALA* 3.8 25.8 - - + -
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Residues in contact with LEU 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B LEU* 3.8 21.5 - - + +
23B PRO* 4.8 11.2 + - + +
29B LYS 3.2 1.2 - - - -
30B ALA* 1.3 76.1 - - - +
32B GLN* 1.3 61.7 + - - +
34B PHE* 3.2 4.7 + - + +
35B ARG* 2.9 43.3 + - - +
51B LEU* 4.0 27.8 - - + -
53B LEU* 4.4 15.3 - - + -
31C LEU* 3.6 31.0 - - + -
53C LEU* 4.3 13.7 - - + -
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Residues in contact with GLN 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B GLY 5.9 0.2 + - - -
29B LYS* 3.0 49.4 + - + +
31B LEU* 1.3 74.4 - - - +
33B LEU* 1.3 61.0 + - - +
35B ARG* 3.1 10.6 + - + +
36B SER* 2.8 34.2 + - - +
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Residues in contact with LEU 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B GLY* 5.4 5.2 - - - +
29B LYS* 2.9 36.5 + - + +
30B ALA* 3.6 11.0 - - - +
32B GLN* 1.3 73.3 - - - +
34B PHE* 1.3 61.6 + - - +
36B SER* 3.7 4.7 - - - +
37B HIS* 2.7 48.6 + - + +
38B VAL 3.5 0.2 + - - -
78B MET* 4.1 3.1 - - + -
109B PRO 5.6 0.7 - - - +
110B ALA* 5.0 14.4 - - + +
131B ASN 6.5 0.4 - - - -
132B GLU* 3.5 32.1 - - + +
135B LEU* 4.0 19.4 - - + +
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Residues in contact with PHE 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B VAL* 4.0 14.8 - - + -
21B LEU* 3.7 11.0 - - + -
30B ALA 2.8 18.2 + - - +
31B LEU* 3.4 7.9 - - + +
33B LEU* 1.3 72.0 - - - +
35B ARG* 1.3 70.0 + - - +
38B VAL* 2.9 35.9 + - + -
39B GLN* 2.7 44.3 + - + -
42B LEU* 3.9 17.7 - - + -
49B PHE* 3.6 44.2 - + - -
51B LEU* 3.9 26.5 - - + -
78B MET* 3.5 19.9 - - + +
108B LEU* 5.4 1.1 - - + -
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Residues in contact with ARG 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B LEU* 2.9 34.0 + - - +
32B GLN* 3.2 13.9 - - + +
34B PHE* 1.3 82.1 - - - +
36B SER* 1.3 62.1 + - - +
39B GLN* 2.9 34.0 + - - +
40B PRO* 3.3 19.6 - - - +
49B PHE* 4.0 2.4 - - - -
51B LEU* 3.8 19.0 - - - +
23C PRO* 4.2 20.0 - - - +
53C LEU* 4.4 3.6 - - - +
55C GLU* 2.7 42.2 + - - -
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Residues in contact with SER 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B GLN* 2.8 24.9 + - - +
33B LEU* 3.6 7.1 + - - +
35B ARG* 1.3 73.2 - - - +
37B HIS* 1.3 86.5 + - - +
40B PRO* 3.4 18.5 - - - +
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Residues in contact with HIS 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B LEU* 2.7 24.4 + - + +
36B SER* 1.3 104.6 + - - +
38B VAL* 1.3 60.1 + - - +
40B PRO* 4.1 3.7 - - - +
41B LEU* 3.6 23.4 + - - +
132B GLU* 3.9 37.5 + - + +
135B LEU* 3.6 20.2 - - + -
136B THR* 3.7 24.8 + - - +
139B THR* 4.3 3.0 + - - -
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Residues in contact with VAL 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B LEU 3.5 0.2 + - - -
34B PHE* 2.9 42.9 + - + +
37B HIS* 1.3 79.2 - - - +
39B GLN* 1.3 67.5 + - - +
40B PRO 3.4 0.4 - - - -
41B LEU* 3.1 16.3 + - - +
42B LEU* 3.1 26.2 + - + +
78B MET* 4.1 7.6 - - - -
108B LEU* 3.9 16.8 - - + -
135B LEU* 3.8 27.8 - - + -
139B THR* 3.5 25.4 - - + +
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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