Contacts of the helix formed by residues 13 - 25 (chain A) in PDB entry 2IHU
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 THR 13 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A LYS 3.7 13.7 - - - +
12A PRO* 1.3 74.4 - - - +
14A ALA* 1.3 65.8 + - - +
15A ALA* 3.3 22.2 + - - +
16A HIS* 3.0 16.2 + - - +
17A ALA* 3.1 11.6 + - - +
40A SER 4.4 2.7 + - - +
45A GLU* 5.6 1.2 + - - +
173A LEU 3.5 1.5 + - - -
174A GLY* 3.5 29.7 - - - +
175A SER 3.3 16.2 - - - -
176A SER* 4.2 3.1 - - - +
179A ILE* 4.3 6.4 - - - +
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Residues in contact with ALA 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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13A THR* 1.3 72.8 - - - +
15A ALA* 1.3 52.5 + - - +
17A ALA* 3.6 3.3 - - - +
18A LEU* 2.8 36.6 + - - +
139A LEU* 4.5 6.3 - - + -
142A PRO* 3.7 24.9 - - + +
145A ILE* 3.8 6.4 - - + +
172A LEU 3.5 23.6 - - - +
173A LEU* 3.5 9.8 + - + +
175A SER 2.9 11.4 + - - +
179A ILE* 4.0 10.4 - - - +
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Residues in contact with ALA 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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13A THR* 3.1 8.5 - - - +
14A ALA* 1.3 76.7 - - - +
16A HIS* 1.3 61.7 + - - +
18A LEU* 3.8 2.7 - - - +
19A LEU* 3.2 31.5 + - - +
40A SER 3.4 24.9 - - - +
41A ILE* 3.7 25.5 - - + +
45A GLU* 4.3 6.3 - - - +
173A LEU* 3.0 21.6 + - + +
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Residues in contact with HIS 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 PRO* 4.0 14.9 - - + +
13A THR* 3.0 22.7 + - - +
15A ALA* 1.3 80.1 - - - +
17A ALA* 1.3 59.5 + - - +
19A LEU 3.5 0.5 + - - -
20A SER* 2.9 45.5 + - - -
45A GLU* 3.6 42.4 + - + +
46A VAL* 3.7 10.7 - - + +
181A THR* 3.8 30.8 - - + +
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Residues in contact with ALA 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 THR 3.1 11.1 + - - +
14A ALA 3.2 6.9 + - - +
16A HIS* 1.3 82.4 - - - +
18A LEU* 1.3 58.0 + - - +
20A SER* 3.9 3.8 - - - -
21A ARG* 3.0 29.1 + - - +
145A ILE* 3.7 18.5 - - + +
146A THR* 4.2 13.9 + - - +
179A ILE* 4.1 21.8 - - + -
181A THR* 5.8 1.6 - - + -
185A ASN* 5.1 2.1 + - - +
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Residues in contact with LEU 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ALA 2.8 15.8 + - - +
15A ALA 3.8 2.7 - - - +
16A HIS 3.2 0.2 - - - -
17A ALA* 1.3 75.0 - - - +
19A LEU* 1.3 63.8 + - + +
21A ARG* 3.3 4.8 + - - +
22A LEU* 3.0 41.1 + - + +
41A ILE* 4.7 4.9 - - + -
78A TRP* 3.7 29.2 - - + -
105A LEU* 3.9 24.7 - - + -
145A ILE* 3.8 18.1 - - + +
149A VAL* 3.6 26.0 - - + +
168A LEU* 3.8 19.3 - - + -
173A LEU* 4.2 12.3 - - + -
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Residues in contact with LEU 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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15A ALA 3.2 17.2 + - - +
18A LEU* 1.3 80.0 - - + +
20A SER* 1.3 57.9 + - - +
22A LEU* 3.4 11.6 + - + +
23A ARG* 3.0 28.8 + - - +
30A VAL* 4.3 18.4 - - + -
41A ILE* 4.1 14.1 - - + -
43A PHE* 3.9 35.2 - - + +
45A GLU* 3.5 35.4 - - + +
46A VAL* 3.8 18.4 - - + +
49A ILE* 4.0 17.8 - - + +
78A TRP* 5.9 0.9 - - + -
105A LEU* 6.4 0.4 - - + -
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Residues in contact with SER 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A HIS* 2.9 32.1 + - - -
17A ALA* 3.9 5.2 - - - -
19A LEU* 1.3 76.1 - - - +
21A ARG* 1.3 56.4 + - - +
23A ARG* 3.4 4.2 + - - +
24A ASP* 3.0 30.9 + - - +
46A VAL* 3.6 21.0 - - - +
185A ASN* 3.6 16.3 + - - -
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Residues in contact with ARG 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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17A ALA 3.0 20.2 + - - +
18A LEU 3.3 3.3 + - - +
20A SER* 1.3 73.8 + - - +
22A LEU* 1.3 64.1 + - - +
24A ASP* 2.8 38.8 + - - +
25A HIS* 3.2 23.0 + - + -
146A THR* 3.7 32.4 - - + +
149A VAL* 3.7 26.9 - - + -
150A ASP* 2.8 36.8 + - - +
185A ASN* 3.4 10.3 - - - +
186A PRO* 2.8 33.5 + - - +
187A PRO 3.3 14.3 + - - -
188A ALA* 3.6 12.0 + - - +
330C ARG* 3.8 5.9 - - - +
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Residues in contact with LEU 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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18A LEU* 3.0 25.4 + - + +
19A LEU* 3.6 13.5 - - + +
21A ARG* 1.3 74.6 - - - +
23A ARG* 1.3 58.5 + - - +
25A HIS* 3.0 17.7 + - + -
27A VAL* 3.1 38.6 + - + +
30A VAL* 4.3 15.3 - - + -
49A ILE* 3.9 9.2 - - + -
76A ALA* 4.2 13.7 - - + -
103A ILE* 4.3 28.5 - - + -
105A LEU* 3.9 23.3 - - + -
149A VAL* 4.2 19.5 - - + +
153A VAL* 5.9 1.1 - - + -
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Residues in contact with ARG 23 (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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19A LEU 3.0 13.2 + - - +
20A SER* 3.5 9.9 - - - +
22A LEU* 1.3 77.2 - - - +
24A ASP* 1.3 63.0 + - - +
26A GLY* 3.0 31.5 + - - -
27A VAL 2.8 42.1 + - - +
28A GLY* 3.9 2.4 - - - +
46A VAL* 4.3 9.6 - - + -
47A GLU 3.8 11.3 + - - +
48A GLY* 3.2 41.0 + - - -
49A ILE* 4.2 5.3 - - + +
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Residues in contact with ASP 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A SER* 3.0 18.7 + - - +
21A ARG* 2.8 42.9 + - - +
23A ARG* 1.3 77.0 - - - +
25A HIS* 1.3 56.1 + - - +
26A GLY 3.3 2.5 + - - -
185A ASN* 2.9 25.3 + - - +
188A ALA* 3.5 18.8 - - + +
190A THR* 4.3 1.4 + - - -
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Residues in contact with HIS 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ARG* 3.2 21.7 + - + -
22A LEU* 3.0 12.0 + - + +
24A ASP* 1.3 75.5 - - - +
26A GLY* 1.3 57.9 + - - +
27A VAL* 3.4 11.6 + - + +
73A ARG* 5.4 3.3 - - - +
74A PRO* 4.6 11.3 - - + +
149A VAL* 3.9 15.9 - - + -
150A ASP* 2.8 31.1 + - + -
153A VAL* 3.9 34.7 - - + +
188A ALA* 3.6 32.0 - - + +
190A THR* 2.8 41.4 + - + +
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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