Contacts of the strand formed by residues 12 - 18 (chain C) in PDB entry 3ZNG
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 12 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28B GLU* 3.5 33.0 - - - +
30B ILE* 5.8 4.3 - - - -
7C ILE 4.1 0.9 + - - +
8C ARG* 3.5 2.4 - - - +
9C ARG* 3.2 35.4 + - - +
10C HIS* 3.1 8.2 + - + +
11C LYS* 1.3 85.5 - - + +
13C THR* 1.3 67.2 + - - +
14C ILE 5.2 0.2 + - - -
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Residues in contact with THR 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B HIS* 4.7 3.1 - - - -
28B GLU 2.8 13.7 + - - +
29B PHE* 3.5 14.3 - - + -
30B ILE* 2.8 29.1 + - - +
6C MET* 4.2 9.6 - - + -
7C ILE 3.5 2.7 - - - +
8C ARG* 3.4 38.8 + - + +
12C THR* 1.3 78.3 + - - +
14C ILE* 1.3 60.7 - - - +
15C PHE* 3.6 28.1 - - + -
93C PHE* 3.9 13.2 - - + -
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Residues in contact with ILE 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B ILE* 3.7 18.2 - - + -
5C LEU 3.7 1.0 - - - +
6C MET* 3.4 4.9 - - - -
7C ILE* 2.7 61.3 + - + +
12C THR 4.4 0.2 - - - -
13C THR* 1.3 72.4 - - - +
15C PHE* 1.3 61.9 + - - +
16C THR* 3.8 5.7 + - + -
31C VAL* 6.4 0.9 - - + -
34C ILE* 6.3 2.2 - - + -
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Residues in contact with PHE 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B TYR* 4.5 5.5 - - - -
29B PHE* 3.5 29.6 - + - -
30B ILE* 2.8 23.7 + - - +
31B VAL* 3.8 26.9 - - + -
32B LYS* 4.3 6.1 + - - +
35B HIS* 5.8 2.9 - - - -
71B SER 3.9 17.7 - - - -
74B CYS* 4.0 10.8 - - + -
75B MET* 3.6 24.7 - - + -
78B THR* 4.3 15.3 - - - +
5C LEU 3.9 3.6 - - - -
6C MET* 3.5 30.7 - - + -
13C THR* 3.6 21.3 - - + -
14C ILE* 1.3 69.6 - - - +
16C THR* 1.3 62.1 + - - +
72C PRO* 4.2 9.0 - - + -
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Residues in contact with THR 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B TYR* 4.0 21.7 + - + -
4C PHE* 3.7 2.7 - - - +
5C LEU* 2.8 40.1 + - + +
7C ILE* 3.8 31.4 - - + -
14C ILE* 4.6 7.4 - - + +
15C PHE* 1.3 75.5 - - - +
17C ASP* 1.3 79.6 + - - +
30C ILE* 4.7 18.2 - - + +
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Residues in contact with ASP 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B TYR* 5.7 0.2 + - - -
35B HIS* 5.7 5.3 + - - -
2C ASP* 4.6 13.2 - - + +
3C VAL 3.2 9.4 - - - +
4C PHE* 3.5 38.0 - - + -
5C LEU* 4.6 0.7 - - - +
16C THR* 1.3 96.6 + - - +
18C ALA* 1.3 64.6 + - - +
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Residues in contact with ALA 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C ASP* 3.6 8.1 + - - -
3C VAL* 2.7 46.1 + - + -
17C ASP* 1.3 76.3 - - - +
19C LYS* 1.3 72.9 + - + +
27C LEU* 5.8 8.3 - - + -
30C ILE* 6.2 4.0 - - + -
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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