Contacts of the helix formed by residues 9 - 22 (chain A) in PDB entry 3ITW
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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7A TYR* 3.3 4.1 - - - +
8A THR* 1.3 83.2 - - + +
10A PRO* 1.4 60.0 - - - +
11A ASP* 3.3 19.9 + - - +
12A ARG* 3.2 29.1 + - + +
13A ALA* 2.9 25.8 + - - +
51A ARG* 5.0 2.7 + - - +
109A LEU* 5.3 1.5 - - + +
110A GLU* 4.4 1.8 + - - -
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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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7A TYR* 3.8 4.9 - - + +
8A THR 3.6 8.7 - - - +
9A ASP* 1.4 87.7 - - - +
11A ASP* 1.3 57.0 + - - +
13A ALA* 4.1 2.7 - - + -
14A VAL* 2.9 36.8 + - - +
35A ILE* 3.4 30.7 - - + +
36A ARG 4.4 2.7 - - - +
49A VAL* 3.9 21.3 - - + -
50A ARG 4.3 1.8 - - - -
51A ARG* 3.8 46.7 - - + +
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Residues in contact with ASP 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* 3.2 11.5 + - - +
10A PRO* 1.3 79.3 - - - +
12A ARG* 1.3 94.8 + - - +
14A VAL* 4.0 2.6 - - - +
15A ASP* 3.3 15.1 + - - +
28A ARG* 4.4 3.9 + - - -
33A GLY 4.7 1.3 - - - +
34A THR* 3.7 24.5 - - - +
35A ILE* 3.2 43.8 + - - +
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Residues in contact with ARG 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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9A ASP* 3.2 31.7 + - + +
11A ASP* 1.3 120.0 + - - +
13A ALA* 1.3 60.0 + - - +
15A ASP* 3.5 22.6 + - - +
16A TRP* 2.9 31.2 + - - +
19A ARG* 5.3 0.5 + - - -
109A LEU* 3.6 15.4 - - + +
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Residues in contact with ALA 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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7A TYR* 3.5 48.0 - - + -
9A ASP 2.9 15.9 + - - +
10A PRO* 3.8 5.2 - - + +
11A ASP 3.4 0.2 - - - -
12A ARG* 1.3 73.6 - - - +
14A VAL* 1.3 60.1 + - - +
16A TRP* 3.4 1.0 + - - +
17A LEU* 2.8 38.1 + - + +
49A VAL* 4.5 3.1 - - + -
109A LEU* 3.9 14.1 - - + +
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Residues in contact with VAL 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 2.9 22.7 + - - +
11A ASP 4.0 3.6 - - - +
13A ALA* 1.3 74.4 - - - +
15A ASP* 1.3 65.0 + - - +
17A LEU* 3.8 0.7 - - - +
18A VAL* 2.9 34.8 + - + +
25A LEU* 3.9 28.3 - - + -
35A ILE* 4.4 13.2 - - + -
38A ALA* 3.6 29.2 - - + -
40A LEU* 4.1 15.5 - - + -
49A VAL* 4.5 14.1 - - + -
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Residues in contact with ASP 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 ASP 3.3 12.4 + - - +
12A ARG* 3.6 26.5 + - - +
14A VAL* 1.3 80.7 - - - +
16A TRP* 1.3 57.0 + - - +
18A VAL* 3.5 4.8 + - - +
19A ARG* 2.9 49.0 + - - +
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Residues in contact with TRP 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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12A ARG 2.9 22.2 + - - +
13A ALA 3.6 3.4 - - - +
15A ASP* 1.3 72.1 - - - +
17A LEU* 1.3 70.5 + - + +
19A ARG* 3.7 27.3 - - - +
20A VAL* 2.8 69.5 + - + +
21A PHE* 3.7 29.4 - + - -
86A ALA 5.7 1.4 + - - -
87A GLY 6.2 0.2 - - - -
88A ALA* 4.0 20.4 - - + +
106A VAL* 4.7 0.4 - - + -
107A ARG 4.3 4.9 - - - -
108A ASP* 3.5 38.1 - - + -
109A LEU* 3.7 35.6 - - + +
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Residues in contact with LEU 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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7A TYR* 3.9 20.0 - - + +
13A ALA* 2.8 26.4 + - - +
14A VAL 3.9 2.2 - - - +
16A TRP* 1.3 87.0 - - + +
18A VAL* 1.3 62.4 + - - +
21A PHE* 3.1 52.1 + - + +
22A GLY 3.4 4.9 + - - -
23A PHE* 3.6 12.3 + - + +
40A LEU* 3.6 28.9 - - + -
47A VAL* 4.6 7.6 - - + -
49A VAL* 3.9 16.6 - - + -
108A ASP* 4.7 1.1 - - + +
109A LEU* 5.8 0.4 - - + -
114A TRP* 3.8 20.4 - - + -
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Residues in contact with VAL 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 VAL* 2.9 26.7 + - + +
15A ASP* 3.8 5.2 - - - +
17A LEU* 1.3 76.4 - - - +
19A ARG* 1.3 60.1 + - - +
22A GLY* 3.0 27.2 + - - -
23A PHE* 3.4 28.7 - - + +
24A ARG* 5.4 0.9 - - - -
25A LEU* 4.3 11.0 - - + +
40A LEU* 4.3 17.7 - - + -
82A ARG* 4.4 1.9 + - - -
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Residues in contact with ARG 19 (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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12A ARG 5.3 0.4 + - - -
15A ASP* 2.9 32.1 + - - +
16A TRP* 3.7 37.6 - - - +
18A VAL* 1.3 79.8 - - - +
20A VAL* 1.3 76.8 + - + +
82A ARG* 3.8 19.2 + - - +
86A ALA* 4.3 21.1 + - + +
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Residues in contact with VAL 20 (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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16A TRP* 2.8 70.6 + - + +
19A ARG* 1.3 87.6 - - - +
21A PHE* 1.3 72.4 + - + +
79A HIS* 5.4 0.7 + - - +
82A ARG* 3.3 24.8 - - - +
83A SER* 4.2 13.8 + - - -
86A ALA* 3.8 24.0 - - + +
88A ALA* 4.0 15.3 - - + +
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Residues in contact with PHE 21 (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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16A TRP* 3.7 25.6 - + - -
17A LEU* 3.1 30.2 + - + +
20A VAL* 1.3 95.8 - - + +
22A GLY* 1.3 61.3 + - - +
23A PHE* 3.5 32.2 + + + -
79A HIS* 4.1 20.7 - - - +
82A ARG* 3.9 9.1 + - - -
83A SER* 3.9 12.6 - - - -
106A VAL* 3.9 14.8 - - + -
114A TRP* 3.5 32.3 - + - -
116A PHE* 3.6 34.8 - + - -
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Residues in contact with GLY 22 (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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17A LEU 3.4 0.2 + - - -
18A VAL* 3.0 18.0 + - - -
20A VAL 3.5 1.8 - - - -
21A PHE* 1.3 78.5 - - - +
23A PHE* 1.3 66.5 + - - +
24A ARG* 4.0 2.8 + - - +
42A THR 6.1 0.5 - - - -
82A ARG* 3.2 26.7 + - - +
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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