Contacts of the helix formed by residues 34 - 39 (chain B) in PDB entry 4UN0
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 THR 34 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B ASP 4.1 2.2 - - - +
31B LEU* 3.3 28.0 + - + +
32B ALA 3.7 1.0 - - - -
33B HIS* 1.3 79.8 - - - +
35B PRO* 1.3 73.7 - - - +
36B SER 3.0 2.1 + - - -
37B GLN* 2.9 19.7 + - - +
38B LEU* 3.0 11.1 + - - +
46B GLU* 2.8 39.6 + - - +
50B ARG* 4.3 2.7 - - - +
82B TYR 4.2 4.5 - - - -
83B MET* 3.8 27.6 - - + -
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Residues in contact with PRO 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A PRO* 5.6 7.9 - - + -
38A LEU* 4.5 15.5 - - + -
84A PHE 4.9 0.2 - - - +
33B HIS 4.2 3.1 - - - +
34B THR* 1.3 84.3 - - - +
36B SER* 1.3 60.5 + - - +
38B LEU* 3.8 14.8 - - + +
39B GLU* 3.5 17.5 + - - +
82B TYR 4.0 1.3 - - - +
83B MET* 3.5 25.6 - - + +
84B PHE* 3.6 4.9 - - - +
85B HIS* 3.4 43.3 - - - +
86B SER* 3.4 14.3 - - - +
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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
----------------------------------------------------------
34B THR 2.9 1.0 + - - -
35B PRO* 1.3 79.2 - - - +
37B GLN* 1.3 61.9 + - - +
39B GLU* 3.1 16.6 + - - +
41B LEU* 3.2 35.0 + - - +
46B GLU* 3.5 25.0 + - - -
82B TYR 4.4 1.2 + - - -
85B HIS 3.6 5.4 + - - -
86B SER* 3.5 12.9 + - - +
87B PHE* 3.1 31.0 + - - -
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Residues in contact with GLN 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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31B LEU 3.7 17.1 + - - -
32B ALA* 2.9 33.0 - - - +
33B HIS* 5.0 0.9 - - - -
34B THR* 2.9 9.5 + - - +
36B SER* 1.3 75.8 - - - +
38B LEU* 1.3 66.4 + - - +
40B GLY* 3.1 13.9 + - - -
41B LEU 3.5 24.0 + - - +
42B ASP 4.8 0.2 - - - -
43B PRO* 3.6 38.7 + - + +
46B GLU* 3.1 22.7 + - - +
722C ARG* 4.4 5.5 + - - -
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Residues in contact with LEU 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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35A PRO* 4.4 17.5 - - + -
38A LEU* 5.4 5.2 - - + -
83A MET 4.4 12.8 - - - +
84A PHE* 3.3 57.7 - - + +
33B HIS* 3.8 36.1 - - + +
34B THR 3.0 16.5 + - - +
35B PRO* 3.8 17.0 - - + +
36B SER 3.2 0.2 - - - -
37B GLN* 1.3 77.9 - - - +
39B GLU* 1.3 57.6 + - - +
40B GLY 3.1 3.0 + - - -
722C ARG* 3.9 9.0 + - - +
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Residues in contact with GLU 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A PHE 3.5 8.3 - - - +
85A HIS* 3.3 41.1 + - + +
86A SER 5.0 1.9 + - - -
89A GLN* 5.2 1.7 - - - +
90A PHE* 4.3 2.3 - - - -
146A ILE* 6.1 0.3 - - - +
35B PRO 3.5 10.1 + - - +
36B SER 3.1 10.2 + - - +
38B LEU* 1.3 75.3 - - - +
40B GLY* 1.3 57.0 + - - +
41B LEU 3.5 1.3 - - - -
86B SER* 2.8 25.7 + - - -
88B LYS* 3.3 34.2 + - + +
89B GLN* 3.1 37.8 + - - +
722C ARG* 4.5 5.1 + - - -
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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