Contacts of the helix formed by residues 2 - 17 (chain C) in PDB entry 1F9N
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 ASN 2 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3C LYS* 1.3 69.1 + - - +
4C GLY 3.2 4.0 + - - +
5C GLN* 3.3 21.5 + - - +
6C ARG* 2.9 30.7 + - + +
34C TYR* 4.7 12.0 - - + -
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Residues in contact with LYS 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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2C ASN* 1.3 78.1 - - - +
4C GLY* 1.3 57.4 + - - +
6C ARG* 3.3 24.4 + - - +
7C HIS* 3.0 51.5 + - + +
43C ARG* 6.3 0.2 - - - +
44C ASP* 5.1 0.9 - - - -
47C GLU* 2.7 39.3 + - - -
149D LEU 5.2 2.9 - - - +
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Residues in contact with GLY 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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2C ASN 3.2 2.0 - - - +
3C LYS* 1.3 79.3 - - - +
5C GLN* 1.3 63.9 + - - +
7C HIS* 2.9 19.1 + - - +
8C ILE* 3.0 17.7 + - - +
146D LEU* 3.4 35.2 + - - -
147D GLU* 5.7 1.2 - - - +
149D LEU* 4.6 3.7 - - - +
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Residues in contact with GLN 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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2C ASN* 3.3 22.8 + - - +
4C GLY* 1.3 74.0 - - - +
6C ARG* 1.3 57.2 + - - +
8C ILE* 3.4 14.1 + - + +
9C LYS* 3.1 27.2 + - - +
34C TYR* 3.7 20.1 + - + +
142D LYS* 5.6 6.1 - - - +
143D ASN* 5.7 2.2 - - - +
146D LEU* 3.9 28.2 - - + +
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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 ASN* 2.9 18.6 + - + +
3C LYS* 3.4 32.3 - - - +
4C GLY 3.0 0.2 - - - -
5C GLN* 1.3 77.5 - - - +
7C HIS* 1.3 63.5 + - - +
9C LYS* 3.2 4.4 + - - +
10C ILE* 3.0 36.2 + - + +
29C LEU* 4.6 12.5 - - + +
34C TYR* 3.8 33.1 - - + -
36C VAL* 4.4 20.4 - - - +
40C THR* 3.5 22.0 - - - +
44C ASP* 2.6 42.2 + - - -
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Residues in contact with HIS 7 (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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3C LYS* 3.0 44.4 + - + +
4C GLY 2.9 9.0 + - - +
6C ARG* 1.3 79.0 - - - +
8C ILE* 1.3 66.9 + - - +
10C ILE* 3.4 8.6 + - + +
11C ARG* 3.2 27.5 + - - +
44C ASP* 3.2 36.6 + - + +
47C GLU* 3.7 16.1 + - + -
48C LEU* 3.8 26.3 - - + +
149D LEU* 2.9 40.3 + - + -
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Residues in contact with ILE 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 GLY 3.0 11.1 + - - +
5C GLN* 3.5 12.8 - - + +
6C ARG 3.2 0.2 - - - -
7C HIS* 1.3 78.3 - - - +
9C LYS* 1.3 62.0 + - + +
11C ARG* 3.1 26.5 - - + +
12C GLU* 3.2 24.0 + - + +
84D PHE* 3.9 28.5 - - + -
86D LYS* 6.3 0.4 - - - -
87D ILE* 4.2 7.0 - - + -
146D LEU* 3.4 32.3 - - + -
149D LEU* 3.5 20.9 - - + -
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Residues in contact with LYS 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 GLN 3.1 10.1 + - - +
6C ARG* 3.2 10.9 + - - +
8C ILE* 1.3 73.0 - - + +
10C ILE* 1.3 66.4 + - - +
11C ARG 3.0 1.6 - - - -
12C GLU* 3.0 33.3 + - + +
13C ILE* 2.9 36.9 + - + +
29C LEU* 4.4 11.0 - - + -
32C ASP* 2.9 30.4 + - - +
34C TYR* 3.7 29.2 - - + +
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Residues in contact with ILE 10 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C ARG* 3.0 24.3 + - + +
7C HIS* 3.7 8.7 - - - +
8C ILE 3.4 0.2 - - - -
9C LYS* 1.3 76.0 - - - +
11C ARG* 1.3 58.7 + - - +
13C ILE* 4.4 7.9 - - - -
14C ILE* 2.9 45.4 + - + +
25C LEU* 4.2 21.3 - - + -
29C LEU* 4.0 27.1 - - + -
41C VAL* 5.5 2.2 - - + -
44C ASP* 3.8 34.8 - - + +
45C ILE* 6.5 0.2 - - + -
48C LEU* 3.8 20.9 - - + -
50C LEU* 4.5 7.0 - - + -
64C LEU* 5.8 0.4 - - + -
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Residues in contact with ARG 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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7C HIS* 3.2 19.4 + - - +
8C ILE* 3.1 18.3 + - + +
9C LYS 3.0 0.2 - - - -
10C ILE* 1.3 74.2 - - - +
12C GLU* 1.3 65.7 + - + +
14C ILE* 3.3 2.6 + - - +
15C THR* 3.0 29.1 + - - +
48C LEU* 5.2 12.6 - - + +
64C LEU* 3.1 49.9 - - + +
65C PRO* 6.3 0.2 - - - +
66C ALA* 5.1 3.0 - - - +
80D LEU 4.2 2.8 + - - -
81D MET* 2.8 42.6 + - - +
82D ASP 5.5 0.6 - - - -
84D PHE* 4.2 36.0 + - - +
149D LEU* 5.7 8.2 - - - +
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Residues in contact with GLU 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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8C ILE* 3.2 26.7 + - + +
9C LYS* 3.0 39.4 + - + +
11C ARG* 1.3 79.4 - - + +
13C ILE* 1.3 53.5 + - + +
15C THR* 3.1 5.6 + - - -
16C SER* 2.8 44.5 + - - +
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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 LYS* 2.9 36.3 + - + +
10C ILE* 3.9 6.5 - - - +
12C GLU* 1.3 72.0 - - + +
14C ILE* 1.3 56.7 + - + +
16C SER* 4.7 0.2 - - - -
17C ASN* 2.6 50.1 + - - +
19C ILE* 3.3 24.4 - - + +
25C LEU* 4.9 5.6 - - + -
28C MET* 3.9 32.1 - - + +
29C LEU* 3.8 32.5 - - + +
32C ASP* 4.9 4.5 - - - +
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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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10C ILE* 2.9 34.7 + - + +
11C ARG* 3.8 4.3 - - - +
13C ILE* 1.3 78.1 - - + +
15C THR* 1.3 61.1 + - - +
17C ASN 3.4 12.7 - - - +
19C ILE* 3.7 27.8 - - + -
25C LEU* 4.7 15.9 - - + -
50C LEU* 4.8 13.0 - - + -
62C TYR* 3.6 31.2 - - + +
63C SER* 4.0 19.5 - - - +
64C LEU* 4.4 8.5 - - + +
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Residues in contact with THR 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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11C ARG 3.0 18.2 + - - -
12C GLU* 3.9 4.3 - - - -
14C ILE* 1.3 79.4 - - - +
16C SER* 1.3 59.9 + - - +
64C LEU* 4.9 14.4 - - - +
56E ASN* 3.5 29.6 - - + +
57E ASN* 3.5 20.7 - - - +
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Residues in contact with SER 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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12C GLU* 2.8 22.2 + - - +
15C THR* 1.3 82.3 - - - +
17C ASN* 1.3 71.4 + - - +
56E ASN* 3.6 17.4 + - - +
57E ASN* 3.3 22.0 - - - +
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Residues in contact with ASN 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* 2.6 32.9 + - - +
14C ILE 3.4 13.3 - - - +
16C SER* 1.3 86.2 - - - +
18C GLU* 1.3 59.4 + - - +
19C ILE* 3.0 24.3 + - + +
28C MET* 3.2 34.1 - - + +
57E ASN* 6.0 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