Contacts of the helix formed by residues 0 - 16 (chain C) in PDB entry 4DDI
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 ALA 0 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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-1C GLY* 1.3 69.6 - - - -
1C MET* 1.3 69.3 + - - +
2C ALA 3.1 2.0 - - - -
3C LEU* 3.5 7.5 + - - +
4C LYS* 2.9 29.9 + - - +
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Residues in contact with MET 1 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1166B SER* 3.5 27.1 - - - +
1170B TYR* 3.5 34.0 + - + +
-1C GLY* 3.3 11.4 - - - +
0C ALA* 1.3 94.7 - - - +
2C ALA* 1.3 56.0 + - - +
4C LYS* 3.3 18.1 - - + +
5C ARG* 2.9 30.3 + - - +
60C TYR 4.8 2.9 - - - +
62C PHE* 6.5 0.4 - - + -
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Residues in contact with ALA 2 (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 GLY* 3.4 17.2 + - - +
0C ALA 3.1 0.6 - - - -
1C MET* 1.3 77.1 - - - +
3C LEU* 1.3 58.3 + - - +
5C ARG* 2.8 20.8 + - - +
6C ILE* 2.9 18.4 + - - +
31C PHE* 4.1 9.9 - - + -
58C THR 3.5 20.9 - - - +
59C ASP* 4.5 0.2 - - - -
60C TYR* 3.5 33.5 + - + +
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Residues in contact with LEU 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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28B ASP* 4.4 9.2 - - - +
-1C GLY 4.0 2.6 + - - +
0C ALA* 3.5 8.1 + - - +
2C ALA* 1.3 78.7 - - - +
4C LYS* 1.3 63.5 + - - +
5C ARG 3.4 0.3 + - - -
6C ILE* 3.6 6.6 + - - +
7C HIS* 2.9 52.5 + - + -
30C MET* 4.1 18.2 - - + -
31C PHE* 3.6 33.5 - - + -
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Residues in contact with LYS 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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0C ALA 2.9 19.7 + - - +
1C MET* 3.3 19.6 - - + +
2C ALA 3.1 0.2 - - - -
3C LEU* 1.3 81.8 - - - +
5C ARG* 1.3 60.0 + - - +
7C HIS* 3.7 12.0 + - - +
8C LYS* 3.5 19.2 - - + +
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Residues in contact with ARG 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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1133B PHE* 4.9 1.8 - - - -
1134B THR* 3.2 29.7 + - - -
1137B ASP* 3.5 26.8 + - - +
1138B PHE* 4.1 4.4 - - - -
1170B TYR* 5.3 3.5 + - - +
1C MET 2.9 12.6 + - - +
2C ALA* 2.8 10.3 + - - +
4C LYS* 1.3 75.5 - - - +
6C ILE* 1.3 60.0 + - - +
7C HIS 3.0 2.2 - - - -
8C LYS* 2.8 33.0 + - - +
9C GLU* 2.8 42.7 + - - +
60C TYR* 3.4 21.9 - - + -
61C PRO* 3.2 34.8 - - + +
95C PRO 3.1 21.2 + - - -
97C LEU 3.6 12.3 + - - -
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Residues in contact with ILE 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 ALA 2.9 13.1 + - - +
3C LEU* 4.0 7.0 - - - +
4C LYS 3.6 0.2 - - - -
5C ARG* 1.3 75.3 - - - +
7C HIS* 1.3 57.0 + - - +
9C GLU* 3.3 9.1 + - + +
10C LEU* 2.9 26.5 + - - +
30C MET* 3.8 27.8 - - + +
31C PHE* 3.6 39.9 - - + -
33C TRP* 3.7 25.9 - - + +
56C PHE* 3.7 33.4 - - + -
60C TYR* 4.2 9.2 - - + -
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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 LEU* 2.9 37.0 + - + +
4C LYS* 3.7 10.3 - - - +
5C ARG 3.0 0.6 - - - -
6C ILE* 1.3 78.3 - - - +
8C LYS* 1.3 60.1 + - + +
10C LEU* 3.2 8.9 + - + +
11C ASN* 2.9 40.7 + - - +
30C MET* 3.3 45.1 - - + +
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Residues in contact with LYS 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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1133B PHE* 3.6 38.8 + - + +
1136B GLU* 4.2 15.2 + - - +
1137B ASP* 3.1 30.5 + - - +
4C LYS* 3.5 22.7 - - + +
5C ARG* 2.8 21.3 + - - +
7C HIS* 1.3 71.4 - - + +
9C GLU* 1.3 56.2 + - - +
11C ASN* 3.2 15.3 + - - +
12C ASP 3.0 23.4 + - - -
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Residues in contact with GLU 9 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1133B PHE* 3.6 18.2 - - + -
5C ARG* 2.8 52.2 + - + +
6C ILE* 3.7 8.3 - - + +
8C LYS* 1.3 77.1 - - - +
10C LEU* 1.3 57.7 + - - +
12C ASP* 3.3 3.6 + - - +
13C LEU* 2.9 28.8 + - - +
33C TRP* 4.8 6.7 - - + -
56C PHE* 5.3 1.8 - - + -
60C TYR* 3.1 25.0 + - + -
97C LEU 3.6 3.1 - - - +
98C THR* 3.5 14.8 + - - +
99C ILE* 2.8 38.4 + - + +
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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
----------------------------------------------------------
6C ILE 2.9 17.8 + - - +
7C HIS* 3.2 8.9 + - + +
9C GLU* 1.3 76.9 - - - +
11C ASN* 1.3 59.7 + - - +
13C LEU* 3.5 7.6 + - + +
14C ALA* 2.9 30.7 + - + +
23C ALA 5.0 3.8 - - - +
24C GLY* 4.8 4.3 - - - -
25C PRO* 4.0 31.0 - - + -
30C MET* 4.2 18.2 - - + -
33C TRP* 3.5 29.6 - - + -
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Residues in contact with ASN 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* 2.9 29.2 + - - +
8C LYS* 3.4 13.8 - - - +
10C LEU* 1.3 78.3 - - - +
12C ASP* 1.3 60.2 + - - +
14C ALA* 3.0 7.9 + - - +
15C ARG* 2.9 30.8 + - - +
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Residues in contact with ASP 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1131B THR* 5.4 3.7 - - - +
1133B PHE* 3.5 41.9 - - + -
8C LYS 3.0 8.6 + - - +
9C GLU 3.5 7.6 - - - +
11C ASN* 1.3 77.5 - - - +
13C LEU* 1.3 61.9 + - - +
14C ALA 3.3 0.3 + - - -
15C ARG* 3.0 37.8 + - - +
16C ASP* 3.7 11.3 + - - +
98C THR* 3.6 19.1 + - - +
100C SER* 3.9 10.7 + - - -
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Residues in contact with LEU 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 GLU 2.9 15.2 + - - +
10C LEU* 3.9 13.5 - - + +
12C ASP* 1.3 77.8 - - - +
14C ALA* 1.3 60.3 + - - +
16C ASP 2.9 22.1 - - - +
17C PRO* 4.1 2.1 - - - +
18C PRO* 3.6 34.5 - - + -
22C SER* 4.5 2.9 - - - -
23C ALA* 4.1 33.2 - - + +
33C TRP* 5.3 9.6 - - + -
98C THR* 6.1 0.2 - - - +
99C ILE* 6.0 2.5 - - + -
100C SER* 4.0 30.5 - - - +
103C LEU* 5.0 8.3 - - + -
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Residues in contact with ALA 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* 2.9 21.7 + - + +
11C ASN* 3.0 12.5 + - - +
13C LEU* 1.3 78.8 - - - +
15C ARG* 1.3 68.1 + - - +
16C ASP 3.2 0.7 + - - -
17C PRO* 4.0 11.4 - - - +
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Residues in contact with ARG 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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1133B PHE* 6.0 0.6 - - - -
11C ASN 2.9 14.6 + - - +
12C ASP* 3.0 33.4 + - - +
14C ALA* 1.3 76.5 - - - +
16C ASP* 1.3 80.4 + - - +
17C PRO* 3.6 6.6 - - - +
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Residues in contact with ASP 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 ASP 3.7 7.4 + - - +
13C LEU* 2.9 18.6 - - - +
15C ARG* 1.3 98.9 + - - +
17C PRO* 1.3 75.2 - - - +
18C PRO* 3.1 9.2 - - - +
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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