Contacts of the helix formed by residues 4 - 11 (chain D) in PDB entry 1I5L
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 ARG 4 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D PRO* 4.3 18.5 + - - +
3D PRO* 1.3 75.0 - - + +
5D PRO* 1.3 74.0 - - + +
6D LEU* 4.8 3.4 - - - +
7D ASP* 3.0 54.8 + - - +
8D VAL* 3.1 9.6 + - - +
34E TYR 3.8 13.8 + - - +
35E ASP* 3.9 5.9 + - - +
41E VAL* 4.2 4.5 - - - -
23J GLY 5.6 4.0 + - - -
24J GLY* 6.1 2.8 - - - -
49J GLN* 2.8 40.5 + - - +
50J ASN* 5.7 4.9 - - - -
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Residues in contact with PRO 5 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D ARG* 1.3 87.5 - - + +
6D LEU* 1.3 65.5 + - + +
8D VAL* 3.0 15.1 + - - +
9D LEU* 3.1 10.4 + - - +
38D MET* 5.1 2.0 - - + -
34E TYR* 3.9 16.8 - - - +
35E ASP* 3.2 25.8 - - - +
39E ASN* 3.6 36.8 - - + +
41E VAL* 3.4 24.0 - - + -
61E VAL* 4.2 17.5 - - + +
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Residues in contact with LEU 6 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D ARG* 3.5 3.9 - - + +
5D PRO* 1.3 79.4 - - + +
7D ASP* 1.3 68.0 + - - +
9D LEU* 3.0 18.4 + - + +
10D ASN 3.0 17.8 + - - -
34D TYR* 3.7 20.2 + - + +
35D ASP 4.5 13.9 - - - +
36D ILE* 4.3 31.0 - - + +
38D MET* 4.1 24.7 - - + -
35E ASP* 4.8 4.9 + - - +
39E ASN* 5.7 1.8 - - - +
50J ASN* 3.7 28.0 - - + +
49K GLN* 5.6 0.2 - - - -
1U U 5.2 2.0 - - - +
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Residues in contact with ASP 7 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D PRO* 5.2 3.0 - - + +
4D ARG* 3.0 50.3 + - + +
6D LEU* 1.3 79.2 - - - +
8D VAL* 1.3 61.9 + - + +
10D ASN* 2.9 11.8 + - - +
11D ARG* 2.9 33.1 + - - +
49K GLN* 4.6 14.1 + - - +
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Residues in contact with VAL 8 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D PRO* 5.4 0.4 - - + -
4D ARG 3.7 12.6 - - - +
5D PRO 3.0 8.7 + - - +
7D ASP* 1.3 73.2 - - + +
9D LEU* 1.3 70.6 + - - +
11D ARG* 3.3 43.8 + - + +
12D SER* 3.1 18.9 + - - +
72D PRO* 5.6 6.7 - - + -
32E ASP* 4.9 4.3 - - - +
41E VAL* 3.9 23.6 - - + -
59E SER* 5.5 8.5 - - - +
61E VAL* 3.8 21.1 - - + -
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Residues in contact with LEU 9 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D PRO 3.1 11.3 + - - +
6D LEU* 3.0 27.0 + - + +
8D VAL* 1.3 76.0 - - - +
10D ASN* 1.3 55.5 + - - +
12D SER* 2.8 35.3 + - - -
13D LEU 3.6 0.7 + - - -
31D LEU* 3.9 23.7 - - + +
34D TYR* 4.0 25.3 - - + -
38D MET* 4.5 15.7 - - + -
40D LEU* 4.1 21.8 - - + -
70D VAL* 4.1 29.6 - - + -
61E VAL* 4.8 13.9 - - + -
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Residues in contact with ASN 10 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D LEU 3.0 3.0 + - - +
7D ASP 2.9 11.5 + - - +
9D LEU* 1.3 74.4 - - - +
11D ARG* 1.3 59.1 + - - +
12D SER 2.6 16.1 + - - -
13D LEU* 3.0 29.5 + - - +
34D TYR* 3.1 30.1 + - - +
49K GLN* 3.1 53.9 + - - +
50K ASN* 3.3 23.9 - - - +
52K GLU* 4.1 3.0 - - - +
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Residues in contact with ARG 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D PRO* 4.6 16.2 - - - +
7D ASP* 2.9 24.7 + - - +
8D VAL* 3.3 40.2 - - + +
9D LEU 3.3 0.4 - - - -
10D ASN* 1.3 78.8 - - - +
12D SER* 1.3 58.9 + - - +
13D LEU 3.7 1.0 - - - +
32E ASP* 4.9 3.2 + - - -
43E LEU* 6.1 3.4 - - - +
50K ASN* 5.7 2.9 - - - +
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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