Contacts of the helix formed by residues 13 - 25 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C LYS 3.6 13.9 - - - +
12C PRO* 1.3 72.8 - - - +
14C ALA* 1.3 64.5 + - - +
15C ALA* 3.3 23.0 + - - +
16C HIS* 3.0 8.5 + - - +
17C ALA* 3.0 20.4 + - - +
40C SER 4.4 3.0 + - - +
45C GLU* 5.7 1.4 - - - +
173C LEU 3.5 6.6 + - - -
174C GLY* 3.5 22.9 - - - +
175C SER 3.3 16.6 - - - -
176C SER* 4.1 3.1 - - - +
179C ILE* 3.6 7.2 - - - +
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Residues in contact with ALA 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C THR* 1.3 76.0 - - - +
15C ALA* 1.3 53.6 + - - +
17C ALA* 3.7 4.8 - - - +
18C LEU* 2.8 37.4 + - - +
139C LEU* 4.5 7.0 - - + -
142C PRO* 3.9 21.5 - - + +
145C ILE* 3.9 6.0 - - + +
172C LEU 3.3 25.1 - - - +
173C LEU* 3.5 9.2 - - + +
175C SER 2.9 8.6 + - - +
179C ILE* 3.3 10.2 - - + +
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Residues in contact with ALA 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C THR* 3.4 8.3 - - - +
14C ALA* 1.3 76.1 - - - +
16C HIS* 1.3 60.7 + - - +
18C LEU* 3.7 2.4 - - - +
19C LEU* 3.2 31.8 + - - +
40C SER 3.3 26.7 - - - +
41C ILE* 3.8 23.4 - - + +
45C GLU* 4.4 7.4 - - - +
173C LEU* 2.9 22.6 + - + +
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Residues in contact with HIS 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C PRO* 3.9 16.3 - - + +
13C THR* 3.0 22.9 + - - +
15C ALA* 1.3 77.8 - - - +
17C ALA* 1.3 61.3 + - - +
19C LEU 3.4 0.5 + - - -
20C SER* 2.9 35.4 + - - -
45C GLU* 3.8 44.7 + - + +
46C VAL* 3.7 10.6 - - + +
181C THR* 4.1 27.1 - - + +
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Residues in contact with ALA 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C THR 3.0 12.4 + - - +
14C ALA* 3.7 5.6 - - - +
16C HIS* 1.3 80.9 - - + +
18C LEU* 1.3 57.2 + - - +
20C SER* 3.8 6.3 - - - -
21C ARG* 3.1 28.8 + - - +
143C HIS 5.9 0.4 - - - +
145C ILE* 3.6 22.3 - - + +
146C THR* 4.4 11.8 + - - +
179C ILE* 4.7 15.9 - - + -
181C THR* 5.7 2.7 - - + -
185C ASN* 5.3 1.4 + - - +
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Residues in contact with LEU 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C ALA 2.8 16.9 + - - +
15C ALA 3.7 2.7 - - - +
17C ALA* 1.3 74.7 - - - +
19C LEU* 1.3 67.0 + - + +
21C ARG* 3.3 3.6 + - - +
22C LEU* 3.0 39.4 + - + +
41C ILE* 4.6 6.1 - - + -
78C TRP* 3.7 31.9 - - + -
105C LEU* 4.0 19.3 - - + -
145C ILE* 3.8 20.1 - - + +
149C VAL* 3.6 25.4 - - + -
168C LEU* 3.8 18.8 - - + -
173C LEU* 4.2 9.4 - - + -
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Residues in contact with LEU 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C ALA 3.2 16.6 + - - +
18C LEU* 1.3 81.8 - - + +
20C SER* 1.3 57.5 + - - +
22C LEU* 3.3 12.1 + - + +
23C ARG* 2.9 29.6 + - - +
30C VAL* 4.3 7.9 - - + -
41C ILE* 3.8 17.0 - - + -
43C PHE* 4.0 33.2 - - + -
45C GLU* 3.4 33.7 - - + +
46C VAL* 3.7 20.9 - - + +
49C ILE* 4.0 28.3 - - + +
78C TRP* 6.0 0.7 - - + -
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Residues in contact with SER 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C HIS* 2.9 27.3 + - - -
17C ALA* 3.8 8.3 - - - -
18C LEU 3.3 0.2 - - - -
19C LEU* 1.3 76.3 - - - +
21C ARG* 1.3 57.3 + - - +
23C ARG* 3.2 5.1 + - - +
24C ASP* 2.9 35.2 + - - +
46C VAL* 3.6 17.7 - - - +
185C ASN* 3.6 16.7 + - - -
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Residues in contact with ARG 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A ARG* 3.9 5.9 - - - +
17C ALA 3.1 19.4 + - - +
18C LEU 3.3 3.8 + - - +
20C SER* 1.3 72.5 - - - +
22C LEU* 1.3 65.0 + - - +
24C ASP* 2.9 32.9 + - - +
25C HIS* 3.1 31.3 + - - -
146C THR* 3.6 31.9 - - + +
149C VAL* 3.8 21.1 - - + -
150C ASP* 2.7 44.7 + - - +
185C ASN* 3.5 8.5 - - - +
186C PRO* 2.8 33.1 + - - +
187C PRO 3.3 14.3 + - - -
188C ALA* 3.7 12.7 - - - +
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Residues in contact with LEU 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C LEU* 3.0 31.0 + - + +
19C LEU* 3.6 22.7 - - + +
21C ARG* 1.3 75.8 - - - +
23C ARG* 1.3 63.4 + - - +
25C HIS* 3.0 15.6 + - + -
26C GLY 3.4 0.3 + - - -
27C VAL* 3.1 31.7 + - + +
30C VAL* 4.5 7.6 - - + -
49C ILE* 3.8 13.9 - - + -
76C ALA* 4.5 9.0 - - + -
103C ILE* 4.2 29.6 - - + -
105C LEU* 3.9 24.0 - - + -
149C VAL* 4.1 18.4 - - + -
153C VAL* 6.1 0.4 - - + -
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Residues in contact with ARG 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C LEU 2.9 14.4 + - - +
20C SER* 3.4 9.9 - - - +
22C LEU* 1.3 75.0 - - - +
24C ASP* 1.3 58.7 + - - +
26C GLY* 3.0 48.4 + - - -
27C VAL 2.7 25.3 + - - +
28C GLY* 4.3 3.2 - - - +
46C VAL* 4.2 11.2 - - + -
47C GLU 3.8 13.9 + - - +
48C GLY* 3.6 33.7 + - - -
49C ILE* 4.1 4.9 - - + +
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Residues in contact with ASP 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C SER* 2.9 19.5 + - - +
21C ARG* 2.9 37.0 + - - +
23C ARG* 1.3 76.5 - - - +
25C HIS* 1.3 57.8 + - - +
26C GLY* 3.2 3.0 + - - -
185C ASN* 2.8 33.5 + - - +
188C ALA* 3.6 18.0 - - + +
190C THR* 4.3 1.4 + - - -
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Residues in contact with HIS 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C ARG* 3.1 27.1 + - - +
22C LEU* 3.0 12.0 + - + +
24C ASP* 1.3 75.8 - - - +
26C GLY* 1.3 59.0 + - - +
27C VAL* 3.4 8.6 + - + +
73C ARG* 5.4 3.3 - - - +
74C PRO* 4.4 12.7 - - + +
149C VAL* 4.0 10.1 - - + -
150C ASP* 2.9 30.6 + - + -
153C VAL* 3.8 43.5 - - + +
188C ALA* 3.5 28.2 - - + +
190C THR* 2.8 37.9 + - + +
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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