Contacts of the helix formed by residues 13 - 25 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B LYS 3.6 14.8 - - - +
12B PRO* 1.3 74.5 - - - +
14B ALA* 1.3 65.1 + - - +
15B ALA* 3.3 19.8 + - - +
16B HIS* 3.1 8.8 + - - +
17B ALA* 3.0 20.6 + - - +
40B SER 4.3 2.6 + - - -
45B GLU* 5.5 0.9 + - - +
173B LEU 3.5 3.6 + - - -
174B GLY* 3.5 27.0 - - - +
175B SER 3.3 17.3 - - - -
176B SER* 4.2 3.6 - - - +
179B ILE* 3.7 5.9 - - - +
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Residues in contact with ALA 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B THR* 1.3 72.8 - - - +
15B ALA* 1.3 53.2 + - - +
17B ALA* 3.7 5.0 - - - +
18B LEU* 2.8 36.2 + - - +
139B LEU* 4.5 6.3 - - + -
142B PRO* 3.8 22.2 - - + +
145B ILE* 3.8 6.2 - - + +
172B LEU 3.4 24.9 - - - +
173B LEU* 3.6 10.5 - - + +
175B SER 2.9 11.6 + - - +
179B ILE* 3.3 9.7 - - + +
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Residues in contact with ALA 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B THR* 3.1 7.2 - - - +
14B ALA* 1.3 77.9 - - - +
16B HIS* 1.3 61.3 + - - +
18B LEU* 3.7 1.8 - - - +
19B LEU* 3.1 31.3 + - - +
40B SER 3.5 24.9 - - - +
41B ILE* 3.7 25.2 - - + +
45B GLU* 4.2 7.4 - - - +
173B LEU* 3.0 20.7 + - + +
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Residues in contact with HIS 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B PRO* 4.0 23.1 - - + +
13B THR* 3.1 22.2 + - - +
15B ALA* 1.3 79.5 - - - +
17B ALA* 1.3 62.3 + - + +
19B LEU 3.5 0.2 + - - -
20B SER* 2.9 39.3 + - - -
45B GLU* 3.5 45.1 + - + +
46B VAL* 3.7 12.3 - - + +
179B ILE* 6.2 0.9 - - + -
181B THR* 4.1 18.2 + - - -
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Residues in contact with ALA 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B THR 3.0 13.1 + - - +
14B ALA* 3.8 8.3 - - - +
16B HIS* 1.3 82.0 - - + +
18B LEU* 1.3 57.6 + - - +
20B SER* 3.6 4.8 + - - -
21B ARG* 3.0 29.6 + - - +
143B HIS 6.0 0.4 - - - +
145B ILE* 3.8 17.4 - - + +
146B THR* 4.3 12.5 + - - +
179B ILE* 4.6 18.6 - - + -
185B ASN* 5.2 1.8 + - - +
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Residues in contact with LEU 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ALA 2.8 21.0 + - - +
15B ALA 3.7 4.3 - - - +
17B ALA* 1.3 70.1 - - - +
19B LEU* 1.3 68.7 + - + +
21B ARG* 3.2 4.9 + - - +
22B LEU* 3.0 40.7 + - + +
41B ILE* 4.8 2.9 - - + -
78B TRP* 3.7 20.0 - - + -
105B LEU* 4.2 18.2 - - + -
145B ILE* 3.9 17.6 - - + +
149B VAL* 3.6 24.0 - - + -
168B LEU* 3.7 36.3 - - + -
173B LEU* 4.3 7.2 - - + -
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Residues in contact with LEU 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ALA 3.1 17.7 + - - +
18B LEU* 1.3 80.6 - - + +
20B SER* 1.3 57.9 + - - +
22B LEU* 3.4 14.1 + - + +
23B ARG* 2.9 29.3 + - - +
30B VAL* 4.4 4.5 - - + -
41B ILE* 4.0 15.0 - - + -
43B PHE* 3.9 37.0 - - + +
45B GLU* 3.4 34.1 - - + +
46B VAL* 3.7 20.0 - - + +
49B ILE* 4.1 27.3 - - + +
78B TRP* 5.9 1.1 - - + -
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Residues in contact with SER 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B HIS* 2.9 29.9 + - - -
17B ALA* 3.8 6.3 - - - -
19B LEU* 1.3 76.6 - - - +
21B ARG* 1.3 58.2 + - - +
23B ARG* 3.4 13.6 + - - +
24B ASP* 3.0 31.3 + - - +
46B VAL* 3.7 19.3 - - - +
185B ASN* 3.6 15.5 + - - -
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Residues in contact with ARG 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B ALA 3.0 18.1 + - - +
18B LEU 3.8 3.1 - - - +
20B SER* 1.3 75.0 - - - +
22B LEU* 1.3 66.3 + - - +
24B ASP* 3.0 32.7 + - - +
25B HIS* 3.1 28.6 + - + -
146B THR* 3.6 28.8 - - + +
149B VAL* 3.8 25.4 - - + -
150B ASP* 2.8 44.5 + - - +
185B ASN* 3.5 10.5 - - - +
186B PRO* 2.8 32.2 + - - +
187B PRO 3.4 13.9 + - - -
188B ALA* 3.6 12.8 - - - +
330D ARG* 3.7 7.1 - - - +
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Residues in contact with LEU 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B LEU* 3.0 27.1 + - + +
19B LEU* 3.6 15.7 - - + +
21B ARG* 1.3 75.6 - - - +
23B ARG* 1.3 62.0 + - - +
25B HIS* 3.1 11.8 + - + +
26B GLY 3.3 0.3 + - - -
27B VAL* 3.1 35.9 + - + +
30B VAL* 4.3 6.5 - - + -
49B ILE* 3.9 20.9 - - + -
76B ALA* 4.3 17.9 - - + -
103B ILE* 4.2 25.4 - - + -
105B LEU* 3.9 22.0 - - + -
149B VAL* 4.2 17.5 - - + +
153B VAL* 6.0 0.7 - - + -
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Residues in contact with ARG 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B LEU 2.9 18.0 + - - +
20B SER* 3.5 17.0 + - - +
21B ARG 3.3 0.2 - - - -
22B LEU* 1.3 75.9 - - - +
24B ASP* 1.3 62.0 + - - +
26B GLY* 2.9 21.1 + - - -
27B VAL 3.6 18.3 + - - +
46B VAL* 3.3 22.6 - - + +
47B GLU* 2.6 47.0 + - - +
48B GLY* 4.5 9.0 - - - +
49B ILE* 4.4 3.5 - - + +
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Residues in contact with ASP 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B SER* 3.0 20.0 + - - +
21B ARG* 3.0 34.5 + - - +
23B ARG* 1.3 83.0 + - - +
25B HIS* 1.3 56.7 + - - +
26B GLY 3.2 3.2 + - - -
185B ASN* 2.9 32.8 + - - +
188B ALA* 3.6 18.1 - - + +
190B THR* 4.3 1.4 + - - -
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Residues in contact with HIS 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ARG* 3.1 22.4 + - + +
22B LEU* 3.1 11.5 + - + +
24B ASP* 1.3 74.1 - - - +
26B GLY* 1.3 59.5 + - - +
27B VAL* 3.4 11.3 + - + +
73B ARG* 5.4 3.6 - - - +
74B PRO* 4.4 12.9 - - + +
149B VAL* 3.9 15.9 - - + -
150B ASP* 2.8 31.1 + - - -
153B VAL* 3.6 38.4 - - + +
154B ASN* 6.1 0.2 - - - -
188B ALA* 3.5 32.4 - - + +
190B THR* 2.7 37.2 + - + +
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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