Contacts of the helix formed by residues 26 - 34 (chain A) in PDB entry 2IT0
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 LEU 26 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A LEU* 4.8 0.3 - - - +
24A THR* 3.0 23.2 + - + +
25A PRO* 1.3 82.4 - - - +
27A ARG* 1.3 67.0 + - - +
28A ALA* 3.9 9.0 - - + +
29A ARG* 3.0 25.7 + - + +
30A ILE* 3.6 6.9 + - - +
59A ASP 4.7 2.5 - - - +
60A ARG* 3.9 9.9 - - + +
61A HIS* 3.9 25.8 - - + +
62A LEU* 4.1 5.1 - - - +
9E G 4.0 35.4 - - - +
10E C 3.4 15.9 - - - +
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Residues in contact with ARG 27 (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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26A LEU* 1.3 72.8 - - - +
28A ALA* 1.3 61.2 + - - +
30A ILE* 3.1 8.0 + - - +
31A ALA* 3.1 19.8 + - - +
41A VAL* 3.6 24.2 - - + +
42A SER* 3.8 30.6 + - - +
45A VAL* 4.0 15.5 - - + +
46A SER* 5.8 1.2 + - - -
56A VAL* 3.7 33.8 - - - +
60A ARG* 3.8 20.2 + - - +
62A LEU* 3.9 25.3 - - + +
10E C 3.5 43.9 + - - +
11E A 3.1 22.1 + - - -
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Residues in contact with ALA 28 (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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26A LEU* 3.0 3.3 - - + -
27A ARG* 1.3 75.9 - - - +
29A ARG* 1.3 72.6 + - - +
31A ALA* 3.4 9.8 + - - +
32A GLU* 3.1 25.6 + - - +
9E G 3.7 37.7 - - + +
10E C 3.0 18.3 + - - +
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Residues in contact with ARG 29 (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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18A LEU* 3.4 27.6 - - + -
23A VAL* 3.7 21.8 - - + -
24A THR 3.5 20.1 + - - +
26A LEU* 3.0 22.8 + - - +
28A ALA* 1.3 82.9 - - - +
30A ILE* 1.3 62.3 + - - +
32A GLU* 2.9 51.1 + - - +
33A ARG* 3.0 33.1 + - - +
9E G 2.9 39.4 + - - -
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Residues in contact with ILE 30 (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 TYR* 4.0 40.6 - - + +
14A THR* 4.4 19.3 - - + -
15A ILE* 3.9 21.3 - - + -
18A LEU* 5.1 2.2 - - + -
26A LEU 4.0 10.1 - - - +
27A ARG* 3.1 7.7 + - - +
29A ARG* 1.3 73.6 - - + +
31A ALA* 1.3 67.6 + - - +
33A ARG 3.1 0.9 + - - +
34A LEU* 2.9 51.6 + - + +
36A GLN* 5.3 0.7 - - - +
41A VAL* 4.6 4.9 - - + -
45A VAL* 4.7 3.4 - - + -
62A LEU* 3.9 25.8 - - + -
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Residues in contact with ALA 31 (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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27A ARG 3.1 12.3 + - - +
28A ALA* 3.4 12.6 - - - +
30A ILE* 1.3 75.3 - - - +
32A GLU* 1.3 57.0 + - + +
35A ASP* 3.1 10.2 + - - -
36A GLN* 2.9 45.1 + - - +
38A GLY* 4.5 11.2 - - - +
41A VAL* 4.0 15.1 - - + +
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Residues in contact with GLU 32 (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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28A ALA 3.1 10.3 + - - +
29A ARG* 2.9 46.5 + - - +
31A ALA* 1.3 78.8 - - + +
33A ARG* 1.3 67.5 + - + +
35A ASP* 3.5 9.5 + - - +
9E G 4.7 2.3 + - - -
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Residues in contact with ARG 33 (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 THR* 4.4 23.1 - - + +
17A ASP* 4.4 9.9 - - - +
18A LEU* 3.2 28.7 - - - +
21A GLU* 2.6 42.6 + - - -
23A VAL* 4.3 7.1 - - - +
29A ARG* 3.0 24.8 + - - +
30A ILE 4.1 1.3 - - - +
32A GLU* 1.3 83.1 + - + +
34A LEU* 1.3 68.7 + - + +
35A ASP* 3.3 1.7 + - - +
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Residues in contact with LEU 34 (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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4A LEU* 4.2 17.9 - - + +
10A MET* 4.0 33.4 - - + -
11A TYR* 3.8 24.0 - - + -
14A THR* 3.9 23.8 - - - +
30A ILE* 2.9 36.7 + - + +
33A ARG* 1.3 87.5 - - + +
35A ASP* 1.3 72.0 + - - +
36A GLN* 3.4 19.1 + - + +
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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