Contacts of the helix formed by residues 9 - 18 (chain A) in PDB entry 4I0A
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 ASP 9 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A THR* 1.3 81.5 + - - +
10A PRO* 1.3 77.2 - - + +
11A THR* 2.8 33.7 + - - -
12A LEU* 3.0 16.4 + - - +
13A GLU* 3.0 26.9 + - - +
116A ARG* 2.8 31.9 + - - -
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Residues in contact with PRO 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A ASP* 1.3 91.4 - - + +
11A THR* 1.3 56.8 + - - +
13A GLU* 4.0 6.6 - - + +
14A TRP* 2.8 30.3 + - - +
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Residues in contact with THR 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A ASP* 2.8 14.7 + - - -
10A PRO* 1.3 77.6 - - - +
12A LEU* 1.3 57.6 + - - +
14A TRP* 3.3 18.0 + - + +
15A PHE* 2.9 25.9 + - - +
110A ASN* 4.0 23.5 + - - +
112A ASP* 3.8 20.6 + - + +
113A ILE* 4.5 15.3 - - + +
116A ARG* 3.7 14.0 + - - +
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Residues in contact with LEU 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A THR* 3.9 26.7 - - - +
9A ASP* 3.0 15.3 + - - +
11A THR* 1.3 76.0 - - - +
13A GLU* 1.4 52.1 + - - +
15A PHE* 3.1 9.3 + - + +
16A LEU* 2.7 45.4 + - + +
42A TYR* 3.4 38.8 - - + +
70A PHE* 4.8 4.7 - - + -
113A ILE* 4.1 20.9 - - + -
116A ARG* 3.8 26.0 - - + +
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Residues in contact with GLU 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A THR* 2.7 35.5 + - + +
9A ASP 3.0 21.8 + - - +
10A PRO* 4.0 6.3 - - + +
12A LEU* 1.4 74.1 - - - +
14A TRP* 1.3 65.0 + - - +
16A LEU* 3.8 20.1 - - - +
17A SER* 2.9 26.5 + - - -
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Residues in contact with TRP 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A PRO 2.8 19.6 + - - +
11A THR* 3.4 23.6 - - + +
13A GLU* 1.3 75.0 - - - +
15A PHE* 1.3 68.2 + - + +
17A SER* 2.8 25.3 + - - -
18A HIS* 3.2 31.4 + + - -
106A LEU* 3.3 49.6 - - + -
109A VAL* 3.9 25.6 - - + +
110A ASN* 3.8 26.0 - - + -
113A ILE* 4.2 22.0 - - + -
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Residues in contact with PHE 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A THR 2.9 14.4 + - - +
12A LEU* 3.1 15.2 + - + +
14A TRP* 1.3 82.6 - - + +
16A LEU* 1.3 85.0 + - + +
18A HIS* 3.1 18.2 + - - +
19A CYS* 3.5 25.6 - - - -
40A LEU* 4.5 2.2 - - + -
41A TYR 5.5 0.7 - - - -
42A TYR* 3.8 18.2 - + + -
70A PHE* 3.6 26.0 - + - -
96A ALA 5.8 0.2 - - - -
98A ILE* 3.9 11.2 - - + -
103A PHE* 3.6 34.3 - + - -
106A LEU* 4.0 15.9 - - + -
113A ILE* 3.7 25.1 - - + -
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Residues in contact with LEU 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A THR* 5.4 0.9 - - - +
12A LEU* 2.7 27.3 + - + +
13A GLU* 3.9 25.8 - - - +
15A PHE* 1.3 82.9 - - + +
17A SER* 1.3 57.5 + - - +
18A HIS 3.0 5.6 - - - -
19A CYS* 2.8 29.9 + - - +
21A ILE* 5.3 8.6 - - + +
42A TYR* 3.8 31.2 - - + -
44A VAL* 4.2 14.6 - - + -
96A ALA* 3.5 30.3 - - + -
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Residues in contact with SER 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A GLU 2.9 14.5 + - - -
14A TRP* 2.8 21.9 + - - -
16A LEU* 1.3 76.2 - - - +
18A HIS* 1.3 66.9 + - - +
19A CYS 3.3 4.9 + - - +
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Residues in contact with HIS 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A TRP* 3.2 48.0 + + - -
15A PHE 3.1 9.0 + - - +
16A LEU 3.0 1.2 - - - -
17A SER* 1.3 83.8 + - - +
19A CYS* 1.3 59.2 + - - +
97A GLU 4.6 0.2 - - - +
98A ILE* 3.8 10.3 - - + +
102A LYS* 3.0 45.7 - - - +
106A LEU* 3.8 30.4 - - + +
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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