Contacts of the helix formed by residues 18 - 28 (chain A) in PDB entry 2H1C
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 ASN 18 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A GLU* 2.8 19.9 + - - +
16A GLN 3.7 0.6 + - - -
17A PRO* 1.3 69.5 - - - +
19A GLU* 1.3 72.2 + - - +
20A ARG* 2.8 41.1 + - - +
21A VAL* 3.0 32.0 + - + +
22A VAL* 3.2 12.9 + - - +
137A TRP* 3.5 27.0 + - - +
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Residues in contact with GLU 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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16A GLN 5.2 0.2 - - - +
17A PRO 3.2 15.4 + - - +
18A ASN* 1.3 79.2 + - - +
20A ARG* 1.3 57.5 + - - +
22A VAL* 3.4 9.2 + - - +
23A ALA* 2.9 30.7 + - - +
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Residues in contact with ARG 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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18A ASN* 2.8 19.8 + - - +
19A GLU* 1.3 76.7 + - - +
21A VAL* 1.3 56.1 + - - +
23A ALA* 3.9 5.4 - - - +
24A TRP* 3.0 27.8 + - + +
136A PRO 3.3 9.9 - - - +
137A TRP* 2.9 35.2 + - - +
138A HIS* 3.9 8.9 - - - +
139A LEU* 3.4 34.3 - - + +
202A SO4 3.2 23.6 + - - -
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Residues in contact with VAL 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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8A VAL* 4.4 8.3 - - + -
11A GLU* 4.2 22.2 - - + -
12A PRO* 5.1 0.2 - - + -
18A ASN* 3.0 20.1 + - + +
20A ARG* 1.3 73.1 - - - +
22A VAL* 1.3 67.9 + - - +
24A TRP* 3.3 2.4 + - - +
25A LEU* 3.0 35.9 + - + +
136A PRO* 3.9 30.5 - - + +
137A TRP* 3.6 43.1 - - + -
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Residues in contact with VAL 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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11A GLU* 5.5 0.2 - - + -
12A PRO* 4.1 21.5 - - + -
17A PRO* 4.1 21.3 - - + -
18A ASN 3.2 13.2 + - - +
19A GLU* 3.7 9.6 - - - +
20A ARG 3.4 0.2 - - - -
21A VAL* 1.3 77.9 - - + +
23A ALA* 1.3 63.3 + - - +
25A LEU* 3.1 11.9 + - - +
26A ASP* 3.0 28.8 + - - +
49B GLY 3.7 24.9 - - - +
50B SER* 4.0 2.7 - - - +
53B ALA* 4.4 9.4 - - + -
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Residues in contact with ALA 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 GLU 2.9 18.7 + - - +
20A ARG* 3.9 5.6 - - - +
22A VAL* 1.3 78.5 - - - +
24A TRP* 1.3 62.5 + - - +
26A ASP* 3.1 19.2 + - - +
27A SER* 3.2 13.5 + - - -
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Residues in contact with TRP 24 (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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2A ILE* 4.1 18.6 - - + -
4A LEU* 3.9 2.5 - - + -
8A VAL* 4.3 3.8 - - + -
20A ARG* 3.0 18.5 + - + +
21A VAL 3.3 3.1 + - - +
23A ALA* 1.3 75.6 - - - +
25A LEU* 1.3 92.9 + - + +
27A SER* 2.7 29.7 + - - -
28A LEU* 3.5 46.7 - - + +
119A ALA* 3.5 32.1 - - + -
134A PHE* 3.2 41.3 - + - -
136A PRO* 3.6 20.2 - - + +
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Residues in contact with LEU 25 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A LEU* 3.9 20.6 - - + -
8A VAL* 3.9 15.5 - - + +
9A ILE* 5.2 0.7 - - - -
12A PRO* 3.5 36.1 - - + -
21A VAL* 3.0 23.6 + - + +
22A VAL 3.5 5.8 - - - +
24A TRP* 1.3 100.9 - - + +
26A ASP* 1.3 61.0 + - - +
28A LEU* 3.3 23.3 + - + +
48B LEU* 3.9 28.8 + - + +
49B GLY* 3.6 18.4 - - - +
52B LEU* 4.5 7.2 - - + -
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Residues in contact with ASP 26 (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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22A VAL* 3.0 21.0 + - - +
23A ALA* 3.1 13.6 + - - +
25A LEU* 1.3 76.8 - - - +
27A SER* 1.3 58.6 + - - +
28A LEU 3.3 1.8 + - - +
46B VAL 4.2 10.9 - - - +
47B ARG* 3.1 53.7 + - + +
49B GLY 2.7 27.0 + - - +
50B SER* 2.7 25.0 + - - -
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Residues in contact with SER 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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23A ALA 3.2 9.1 + - - -
24A TRP* 2.7 31.6 + - - -
26A ASP* 1.3 77.5 - - - +
28A LEU* 1.3 67.8 + - - +
29A ILE* 3.9 10.2 + - - +
47B ARG* 5.7 0.2 - - - +
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Residues in contact with LEU 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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2A ILE* 4.7 10.8 - - + -
4A LEU* 4.5 5.2 - - + -
24A TRP* 3.5 62.4 - - + +
25A LEU* 3.3 23.2 + - + +
26A ASP 3.3 2.8 - - - +
27A SER* 1.3 84.4 - - - +
29A ILE* 1.3 63.8 + - - +
30A LEU* 3.5 2.5 + - - -
33A VAL* 3.8 28.0 - - + -
46B VAL 3.8 16.5 - - - +
48B LEU* 4.9 4.9 - - + +
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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