Contacts of the helix formed by residues 8 - 19 (chain C) in PDB entry 1NTZ
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 HIS 8 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4C ILE* 3.1 22.6 + - + +
7C SER* 1.3 79.6 + - - +
9C PRO* 1.3 74.8 - - + +
10C LEU* 3.5 22.7 - - + +
11C MET* 3.1 43.4 + - + -
12C LYS* 2.7 35.1 + - - +
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Residues in contact with PRO 9 (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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7C SER 3.4 6.7 - - - +
8C HIS* 1.3 98.1 - - + +
10C LEU* 1.3 59.4 + - + +
12C LYS* 3.7 24.3 - - - +
13C ILE* 3.5 19.6 - - - +
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Residues in contact with LEU 10 (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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8C HIS* 3.2 20.7 + - + +
9C PRO* 1.3 79.3 - - + +
11C MET* 1.3 66.2 + - + +
12C LYS 3.4 0.5 + - - -
13C ILE* 3.4 21.4 + - + +
14C VAL* 3.4 14.8 - - + +
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Residues in contact with MET 11 (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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4C ILE* 4.4 22.9 - - + +
5C ARG* 3.5 37.0 - - + +
8C HIS* 3.1 27.5 + - + -
10C LEU* 1.3 74.1 - - + +
12C LYS* 1.4 54.6 + - - +
14C VAL* 2.9 15.2 + - + +
15C ASN* 2.8 33.8 + - - +
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Residues in contact with LYS 12 (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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5C ARG 3.4 9.0 + - - -
6C LYS* 3.2 22.0 - - - +
7C SER* 3.4 20.7 + - - +
8C HIS 2.7 19.5 + - - +
9C PRO* 3.7 22.4 - - - +
11C MET* 1.4 68.4 - - - +
13C ILE* 1.3 60.2 + - + +
15C ASN* 3.0 4.1 + - - +
16C ASN* 2.7 53.7 + - - +
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Residues in contact with ILE 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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9C PRO 3.5 18.6 - - - +
10C LEU* 3.6 14.8 - - + +
11C MET 3.2 0.2 - - - -
12C LYS* 1.3 86.3 - - + +
14C VAL* 1.3 62.7 + - + +
16C ASN* 3.8 8.3 - - - +
17C ALA* 3.2 28.3 + - + +
18C PHE* 5.7 0.2 - - - -
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Residues in contact with VAL 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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10C LEU* 3.4 19.7 - - + +
11C MET* 3.3 14.4 - - + +
13C ILE* 1.3 74.9 - - + +
15C ASN* 1.3 56.8 + - - +
17C ALA 3.0 0.9 + - - -
18C PHE* 2.7 60.3 + - + -
19C ILE* 3.7 11.3 + - + +
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Residues in contact with ASN 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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5C ARG* 2.7 54.3 + - + +
6C LYS* 4.3 16.4 - - - +
11C MET 2.8 14.7 + - - +
12C LYS* 3.3 7.6 - - - +
14C VAL* 1.3 71.9 - - - +
16C ASN* 1.3 71.6 + - - +
19C ILE* 3.1 23.7 + - + +
20C ASP* 3.0 45.9 + - - +
21C LEU 3.8 0.9 + - - -
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Residues in contact with ASN 16 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12C LYS* 2.7 41.1 + - - +
13C ILE* 4.0 6.4 - - - +
15C ASN* 1.3 85.0 + - - +
17C ALA* 1.3 58.4 + - - +
20C ASP* 5.6 2.2 - - - +
21C LEU* 3.7 25.8 - - - +
201C HIS* 4.2 7.1 + - - -
1G GLY 5.6 2.5 - - - +
3G GLN* 6.1 0.7 - - - +
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Residues in contact with ALA 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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13C ILE* 3.2 18.1 + - + +
14C VAL 3.0 3.1 + - - +
16C ASN* 1.3 80.9 - - - +
18C PHE* 1.3 87.9 + - + +
19C ILE 4.0 0.2 - - - -
21C LEU* 3.5 21.0 - - - +
197C LEU* 5.8 2.0 - - + -
201C HIS* 3.6 24.8 + - + +
220C PHE* 4.8 1.2 - - - -
384C UQ2 4.6 3.8 - - - +
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Residues in contact with PHE 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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14C VAL* 2.7 43.0 + - + +
17C ALA* 1.3 100.0 - - + +
19C ILE* 1.3 68.4 + - + +
197C LEU* 4.9 5.6 - - + -
220C PHE* 3.1 37.6 - + + -
221C HIS* 3.6 9.2 - - - +
225C THR* 3.8 6.6 - - + +
384C UQ2 3.6 52.9 - - + -
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Residues in contact with ILE 19 (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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436A ARG* 3.0 44.4 + - - +
5C ARG* 3.8 14.4 - - + +
14C VAL* 3.8 11.4 - - + +
15C ASN* 3.1 33.7 + - + +
17C ALA 4.0 0.2 - - - -
18C PHE* 1.3 89.5 - - + +
20C ASP* 1.3 64.1 + - - +
21C LEU 3.3 2.0 - - - +
219C PRO* 4.0 0.2 - - - +
220C PHE 3.6 2.7 + - - -
221C HIS* 3.0 34.8 + - + -
225C THR* 5.9 1.1 - - + -
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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