Contacts of the strand formed by residues 36 - 40 (chain J) in PDB entry 1ZUM
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 36 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34J ARG 4.3 7.0 - - - +
35J LYS* 1.3 80.0 - - - +
37J PHE* 1.3 58.6 + - - +
38J PRO* 4.6 0.9 - - - +
50J GLN* 2.8 41.1 + - + +
51J VAL 3.0 25.3 + - - -
52J ALA* 4.5 1.8 - - - -
53J GLU* 3.9 8.2 - - - +
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Residues in contact with PHE 37 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36J THR* 1.3 73.8 - - - +
38J PRO* 1.3 79.7 - - + +
39J THR* 5.0 0.2 - - - -
50J GLN* 3.3 4.9 - - - -
51J VAL* 2.7 64.9 + - + +
52J ALA 3.5 18.6 - - - -
53J GLU* 3.8 20.4 - - + +
195J GLU* 3.4 40.2 - - + -
198J PRO* 4.3 8.7 - - + -
222J PRO* 4.4 1.1 - - + -
223J GLY* 3.7 25.1 - - - -
224J PHE* 3.7 29.8 - + + -
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Residues in contact with PRO 38 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36J THR 4.6 0.9 - - - +
37J PHE* 1.3 100.1 - - + +
39J THR* 1.3 60.0 + - - +
40J VAL* 4.1 7.1 + - + +
47J VAL* 3.8 30.1 - - + -
49J CYS 3.5 7.0 - - - +
50J GLN* 3.3 15.9 - - - +
195J GLU 4.8 1.0 - - - +
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Residues in contact with THR 39 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37J PHE* 3.9 1.1 + - - -
38J PRO* 1.3 74.7 - - - +
40J VAL* 1.3 54.2 + - - +
47J VAL* 3.7 1.6 - - - -
48J ILE* 2.8 36.1 + - + +
49J CYS* 3.1 17.7 + - - +
51J VAL* 4.0 17.0 - - + -
109J ASP* 2.8 24.2 + - - +
195J GLU 3.8 11.1 + - - -
196J GLN 3.5 11.1 + - - -
198J PRO* 3.6 8.2 - - - +
199J LEU* 3.9 27.4 - - + -
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Residues in contact with VAL 40 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38J PRO* 4.2 8.3 + - + +
39J THR* 1.3 78.2 + - - +
41J ASN* 1.3 75.6 + - - +
42J PRO* 3.2 6.3 - - - +
45J GLY* 3.5 22.4 - - - +
46J GLU 3.4 11.2 - - - +
47J VAL* 4.3 18.8 - - + -
48J ILE* 4.0 3.4 - - - -
109J ASP* 3.6 2.1 - - - +
196J GLN* 6.1 0.4 - - - +
345J VAL 5.2 0.7 - - - +
379J TYR* 4.1 15.3 - - + +
3710J NA 2.4 28.6 - - - -
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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