Contacts of the strand formed by residues 36 - 40 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34L ARG 4.6 6.1 - - - +
35L LYS* 1.3 79.7 - - - +
37L PHE* 1.3 58.7 + - - +
38L PRO* 4.5 0.9 - - - +
50L GLN* 2.7 44.7 + - + +
51L VAL 2.9 26.9 + - - -
52L ALA* 4.5 1.1 - - - -
53L GLU* 3.9 7.4 - - - +
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Residues in contact with PHE 37 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36L THR* 1.3 73.7 - - - +
38L PRO* 1.3 80.1 - - + +
39L THR* 4.8 0.2 - - - -
50L GLN* 3.1 4.3 - - - -
51L VAL* 2.7 58.3 + - + +
52L ALA 3.4 19.5 - - - -
53L GLU* 3.8 15.9 - - + +
195L GLU* 3.4 39.7 - - + -
198L PRO* 4.3 8.7 - - + -
222L PRO* 4.4 1.8 - - + -
223L GLY* 3.8 22.7 - - - -
224L PHE* 3.5 34.1 - + + -
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Residues in contact with PRO 38 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36L THR 4.5 0.9 - - - +
37L PHE* 1.3 99.7 - - + +
39L THR* 1.3 60.2 + - - +
40L VAL* 4.2 6.6 + - + +
47L VAL* 3.8 30.7 - - + -
49L CYS 3.6 6.1 - - - +
50L GLN* 3.6 16.2 - - - +
195L GLU 4.7 1.2 - - - +
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Residues in contact with THR 39 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37L PHE* 3.9 0.9 + - - -
38L PRO* 1.3 74.8 - - - +
40L VAL* 1.3 60.8 + - - +
47L VAL* 3.7 1.2 - - - -
48L ILE* 2.8 40.6 + - + +
49L CYS* 3.1 17.3 + - - +
51L VAL* 4.0 16.2 - - + -
109L ASP* 2.6 24.3 + - - +
195L GLU 3.9 6.7 + - - -
196L GLN* 3.5 6.8 + - - +
198L PRO* 3.6 13.3 - - - +
199L LEU* 4.0 18.4 - - + -
3712L NA 3.3 5.4 - - - -
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Residues in contact with VAL 40 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38L PRO* 5.0 7.2 - - + +
39L THR* 1.3 80.6 + - - +
41L ASN* 1.3 75.9 + - - +
42L PRO* 3.1 8.9 - - + +
45L GLY* 3.4 29.8 - - - +
46L GLU 3.5 3.1 - - - +
47L VAL* 4.3 19.7 - - + -
48L ILE* 3.9 2.9 - - - -
109L ASP* 3.8 0.7 - - - +
196L GLN* 6.1 0.2 - - - +
345L VAL 5.2 0.2 - - - +
379L TYR* 4.4 14.8 - - + +
3712L NA 2.4 29.8 - - - -
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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