Contacts of the strand formed by residues 36 - 40 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30H ASP* 6.1 1.8 - - + +
34H ARG 3.9 9.2 + - - +
35H LYS* 1.3 81.7 - - - +
37H PHE* 1.3 62.2 + - - +
38H PRO* 4.7 0.3 - - - +
50H GLN* 2.8 39.0 + - + +
51H VAL* 3.1 14.6 - - - +
52H ALA* 4.1 9.2 - - + +
53H GLU* 3.9 9.4 - - - +
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Residues in contact with PHE 37 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36H THR* 1.3 74.4 - - - +
38H PRO* 1.3 80.0 - - + +
39H THR* 4.9 0.4 - - - -
50H GLN* 3.4 5.3 - - - -
51H VAL* 2.7 70.5 + - + +
52H ALA 3.4 19.1 - - - -
53H GLU* 3.8 20.2 - - + +
195H GLU* 3.4 37.9 - - + -
198H PRO* 4.4 6.5 - - + -
222H PRO* 4.4 2.7 - - + -
223H GLY* 3.6 28.3 - - - -
224H PHE* 3.6 31.4 - + + -
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Residues in contact with PRO 38 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36H THR 4.7 0.7 - - - +
37H PHE* 1.3 100.0 - - + +
39H THR* 1.3 61.4 + - - +
40H VAL* 4.2 8.1 + - + +
47H VAL* 3.8 31.2 - - + -
49H CYS 3.5 6.5 - - - +
50H GLN* 3.9 14.6 - - - +
195H GLU 4.7 1.7 - - - +
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Residues in contact with THR 39 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37H PHE* 3.9 0.8 + - - -
38H PRO* 1.3 74.4 - - - +
40H VAL* 1.3 55.0 + - - +
47H VAL* 3.7 1.4 - - - -
48H ILE* 2.8 36.9 + - + +
49H CYS* 3.1 13.8 + - - +
51H VAL* 4.1 11.7 - - + -
109H ASP* 2.7 21.6 + - - +
195H GLU 3.8 6.9 + - - -
196H GLN* 3.3 8.0 + - - +
198H PRO* 3.6 16.5 - - - +
199H LEU* 3.7 33.4 - - + -
3708H NA 3.2 7.1 - - - -
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Residues in contact with VAL 40 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38H PRO* 4.8 9.2 - - + +
39H THR* 1.3 80.5 + - - +
41H ASN* 1.3 67.5 + - - +
42H PRO* 3.2 7.1 - - - +
45H GLY* 3.4 29.2 - - - +
46H GLU 3.2 14.8 - - - +
47H VAL* 4.5 15.0 - - + -
48H ILE* 3.9 3.4 - - - -
109H ASP* 3.7 1.4 - - - +
196H GLN* 6.1 0.2 - - - +
345H VAL 5.3 0.7 - - - +
379H TYR* 4.3 12.3 - - + +
3708H 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