Contacts of the helix formed by residues 12 - 24 (chain A) in PDB entry 4HE2
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 12 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A LEU* 1.3 80.4 - - - +
13A LEU* 1.3 60.9 + - - +
14A THR* 4.9 0.2 - - - -
15A ARG* 3.3 36.3 + - - +
16A TYR* 2.8 30.6 + - - +
184A PHE* 5.1 0.2 - - - -
190A LEU* 4.0 26.0 - - + -
192A GLU* 3.2 26.9 + - + +
193A PHE 3.2 10.1 - - - +
194A VAL* 4.3 4.0 - - + +
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Residues in contact with LEU 13 (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 LEU 4.0 0.4 + - - -
12A THR* 1.3 68.9 - - - +
14A THR* 1.3 61.7 + - - +
16A TYR* 3.2 4.5 + - + +
17A VAL* 2.8 50.5 + - + +
38A LEU* 3.5 41.3 - - + -
173A VAL* 4.5 6.1 - - + -
175A LEU* 4.3 6.1 - - + -
184A PHE* 3.6 43.3 - - + -
192A GLU* 4.6 0.4 + - - +
193A PHE* 2.7 49.5 + - + +
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Residues in contact with THR 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A THR* 3.4 1.0 + - - -
13A LEU* 1.3 78.1 - - - +
15A ARG* 1.3 59.5 + - + +
17A VAL* 3.8 5.9 - - + +
18A MET* 2.9 55.3 + - + +
35A ASN* 3.8 26.8 + - + +
38A LEU* 6.0 2.4 - - - +
42A LYS* 5.9 1.0 + - - -
192A GLU* 3.8 20.1 + - - -
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Residues in contact with ARG 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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11A LEU* 5.2 15.1 - - + +
12A THR* 3.3 32.0 + - - +
13A LEU 3.3 0.2 - - - -
14A THR* 1.3 79.3 - - + +
16A TYR* 1.3 56.9 + - - +
18A MET* 3.4 9.1 + - - +
19A GLU* 2.9 31.2 + - - +
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Residues in contact with TYR 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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11A LEU* 3.5 26.6 - - + +
12A THR 2.8 18.4 + - - +
13A LEU* 3.4 9.0 - - - +
15A ARG* 1.3 76.7 - - - +
17A VAL* 1.3 61.7 + - + +
19A GLU* 3.3 7.3 + - + +
20A LYS* 2.9 62.6 + - + +
175A LEU* 5.8 4.0 - - + -
182A ASP* 2.7 36.3 + - - -
184A PHE* 3.6 25.1 - + + -
195A LEU* 4.2 17.0 - - + -
198A LYS* 3.9 21.8 + - + +
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Residues in contact with VAL 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LEU* 2.8 43.8 + - + +
14A THR* 3.9 5.4 - - + +
16A TYR* 1.3 74.3 - - + +
18A MET* 1.3 56.7 + - + +
20A LYS* 3.4 4.6 + - - +
21A GLY 2.9 11.6 + - - -
31A THR* 4.2 14.6 - - + +
34A LEU* 3.8 25.8 - - + -
35A ASN* 5.0 2.9 - - + +
38A LEU* 4.2 13.0 - - + -
175A LEU* 4.2 14.4 - - + -
401A AMP 2.8 38.9 + - - +
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Residues in contact with MET 18 (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* 2.9 41.3 + - + +
15A ARG* 3.9 7.6 - - - +
17A VAL* 1.3 76.1 - - + +
19A GLU* 1.3 57.4 + - - +
21A GLY* 3.3 1.8 + - - +
22A ARG* 3.0 27.4 + - - +
31A THR* 3.8 25.5 + - + -
35A ASN* 5.7 5.4 - - + +
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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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15A ARG 2.9 18.6 + - - +
16A TYR* 3.6 7.6 - - + +
18A MET* 1.3 75.4 - - - +
20A LYS* 1.3 61.1 + - + +
22A ARG* 2.8 46.5 + - - +
23A GLN* 2.9 48.1 + - - +
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Residues in contact with LYS 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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16A TYR* 2.9 54.7 + - + +
17A VAL* 3.7 4.0 - - - +
19A GLU* 1.3 75.9 - - + +
21A GLY* 1.3 56.9 + - - +
23A GLN* 3.4 25.6 + - - +
24A ALA* 3.0 30.0 + - - +
177A THR* 3.6 9.2 + - - +
179A GLN* 3.1 39.0 + - - +
182A ASP* 4.7 4.8 + - - -
401A AMP 3.4 22.4 + - - +
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Residues in contact with GLY 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 VAL 2.9 10.3 + - - -
18A MET 3.3 4.5 + - - -
19A GLU 3.2 0.2 - - - -
20A LYS* 1.3 74.7 - - - +
22A ARG* 1.3 63.0 + - - +
24A ALA* 3.3 1.7 + - - -
25A LYS 3.1 3.3 + - - -
26A GLY* 3.1 29.4 + - - +
31A THR* 3.7 8.3 - - - -
401A AMP 3.4 27.7 + - - -
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Residues in contact with ARG 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 MET 3.0 14.2 + - - +
19A GLU* 2.8 46.9 + - - +
21A GLY* 1.3 76.4 - - - +
23A GLN* 1.3 73.1 + - - +
25A LYS* 3.2 18.5 + - - +
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Residues in contact with GLN 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 49.3 + - - +
20A LYS* 3.7 29.2 - - - +
21A GLY 3.3 0.2 - - - -
22A ARG* 1.3 86.6 + - - +
24A ALA* 1.3 59.8 + - - +
25A LYS* 3.1 14.8 + - - -
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Residues in contact with ALA 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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20A LYS 3.0 17.6 + - - +
21A GLY 3.3 4.5 + - - +
22A ARG 3.3 0.4 - - - -
23A GLN* 1.3 74.3 - - - +
25A LYS* 1.3 70.5 + - - +
26A GLY* 3.2 0.9 + - - -
401A AMP 3.6 41.6 - - + +
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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