Contacts of the helix formed by residues 2 - 13 (chain C) in PDB entry 4NTX
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 LEU 2 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1C ASN* 1.3 77.0 + - - +
3C ASN* 1.3 59.4 + - - +
5C PHE* 3.7 11.2 - - + +
6C ARG* 2.9 29.1 + - - +
17C TRP* 4.1 19.9 - - + -
28C VAL* 4.3 37.0 - - + +
29C ALA* 4.7 1.1 - - + -
50C TYR* 3.4 35.9 - - + +
62C LEU* 4.0 21.9 + - + +
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Residues in contact with ASN 3 (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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320A GLU* 3.2 25.9 - - + +
321A ASN* 3.4 11.0 + - - +
322A CYS* 4.4 1.0 - - - +
323A ASN* 2.9 39.5 + - - +
1C ASN* 2.5 25.9 + - - +
2C LEU* 1.3 80.4 - - - +
4C GLN* 1.3 65.6 + - - +
6C ARG* 3.5 8.3 + - - +
7C LEU* 3.1 33.3 + - - +
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Residues in contact with GLN 4 (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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321A ASN* 2.7 54.2 + - - +
1C ASN* 2.8 40.8 + - - +
3C ASN* 1.3 74.3 - - - +
5C PHE* 1.3 59.4 + - - +
7C LEU* 3.2 5.2 + - + -
8C MET* 2.8 31.9 + - - +
64C MET 3.5 3.1 - - - +
65C PHE* 4.2 3.0 - - - -
66C TYR* 3.3 58.9 + - + +
68C PHE* 3.6 11.1 - - + -
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Residues in contact with PHE 5 (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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1C ASN 3.2 3.8 + - - -
2C LEU* 3.7 17.0 - - + +
3C ASN 3.3 0.2 - - - -
4C GLN* 1.3 77.9 - - - +
6C ARG* 1.3 58.2 + - - +
8C MET* 3.1 7.2 + - + +
9C ILE* 2.9 58.7 + - + +
17C TRP* 3.2 29.2 - + - -
28C VAL* 4.0 23.8 - - + -
43C CYS* 6.3 2.0 - - - -
46C GLN* 3.7 30.5 - - - -
66C TYR* 4.1 1.6 - - - -
94C ASP* 3.0 42.2 + - + +
97C ALA* 3.8 8.7 - - + -
98C THR* 4.1 5.6 - - - -
101C ILE* 4.0 14.8 - - + -
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Residues in contact with ARG 6 (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 LEU 2.9 16.5 + - - +
3C ASN* 3.7 7.9 - - - +
5C PHE* 1.3 79.7 - - - +
7C LEU* 1.3 61.4 + - + +
9C ILE* 3.4 5.5 + - - +
10C LYS* 3.1 24.8 + - + +
16C VAL* 6.0 2.2 - - - +
17C TRP* 3.3 72.1 - - + +
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Residues in contact with LEU 7 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A GLU* 3.1 33.0 - - + +
321A ASN* 4.2 17.5 - - - +
29B SER 5.1 8.5 - - - +
30B ARG* 4.1 16.8 - - - +
31B ILE* 3.4 23.3 - - + +
3C ASN 3.1 19.7 + - - +
4C GLN* 3.6 5.8 - - + +
5C PHE 3.1 0.2 - - - -
6C ARG* 1.3 77.9 - - + +
8C MET* 1.3 60.1 + - - +
9C ILE 3.1 1.3 - - - -
10C LYS* 3.1 14.2 + - + +
11C CYS 2.8 25.1 + - - -
68C PHE* 3.8 15.9 - - + -
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Residues in contact with MET 8 (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 GLN 2.8 18.3 + - - +
5C PHE* 3.4 9.2 - - + +
7C LEU* 1.3 72.6 - - - +
9C ILE* 1.3 63.5 + - - +
11C CYS* 3.2 15.5 - - - +
12C THR* 3.3 12.3 + - - +
66C TYR* 3.8 12.3 - - + +
68C PHE* 3.5 28.2 - - + -
77C LEU* 3.6 25.2 - - + +
91C CYS* 3.3 41.5 - - - +
94C ASP* 3.4 14.4 - - - +
95C ARG* 3.4 24.7 - - + +
98C THR* 3.5 14.1 + - + -
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Residues in contact with ILE 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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5C PHE* 2.9 57.0 + - + +
6C ARG 3.6 7.4 - - - +
8C MET* 1.3 75.2 - - - +
10C LYS* 1.3 55.3 + - - +
12C THR* 3.0 5.2 + - - -
13C ASN* 2.7 52.0 + - + +
15C ARG 4.3 6.1 - - - +
17C TRP* 4.1 17.7 - - + -
20C PHE* 4.2 27.8 - - + -
98C THR* 3.7 12.3 - - - +
101C ILE* 3.9 16.4 - - + -
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Residues in contact with LYS 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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3B ARG* 3.1 17.6 + - - -
30B ARG 5.4 0.8 + - - -
31B ILE* 3.3 25.0 + - + +
32B THR* 4.3 4.2 - - - -
59B HIS* 2.8 51.2 + - - +
60B GLY* 5.6 0.2 - - - -
6C ARG* 3.1 11.3 + - + +
7C LEU* 3.1 20.3 + - + +
9C ILE* 1.3 80.5 - - - +
11C CYS* 1.3 63.0 + - - +
12C THR 3.1 0.9 + - - -
13C ASN 3.6 18.1 + - - +
14C ASP* 5.6 0.2 - - - +
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Residues in contact with CYS 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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2B ILE* 3.6 4.7 - - - +
3B ARG* 2.7 24.0 + - - +
8B TYR* 4.2 1.6 + - - -
31B ILE* 3.9 10.3 - - + +
7C LEU 2.8 13.2 + - - +
8C MET* 3.2 18.4 - - - +
9C ILE 3.1 0.2 - - - -
10C LYS* 1.3 77.0 - - - +
12C THR* 1.3 58.5 + - - +
68C PHE* 4.3 1.6 - - + -
70C CYS* 2.0 59.8 - - + -
71C ARG 4.2 5.6 - - - +
74C ALA* 6.1 1.1 - - - -
77C LEU* 4.1 16.8 - - - -
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Residues in contact with THR 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B ILE* 3.5 21.6 - - - +
8C MET 3.3 9.4 + - - +
9C ILE 3.0 9.9 + - - -
11C CYS* 1.3 86.5 - - - +
13C ASN* 1.3 61.8 + - - +
74C ALA* 3.8 30.7 - - + +
77C LEU* 4.0 19.5 - - + -
98C THR* 3.1 21.2 + - + +
99C LEU* 5.3 0.7 - - + -
102C LEU* 3.4 27.9 - - + +
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Residues in contact with ASN 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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2B ILE* 3.5 9.4 - - - +
9C ILE* 2.7 30.7 + - + +
10C LYS* 3.6 20.0 + - - +
12C THR* 1.3 85.0 - - - +
14C ASP* 1.3 64.6 + - - +
15C ARG* 2.5 42.3 + - - +
20C PHE* 4.2 5.9 - - - -
101C ILE* 3.7 28.3 + - - +
102C LEU* 4.3 12.0 - - + +
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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