Contacts of the helix formed by residues 17 - 23 (chain A) in PDB entry 4U0L
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 GLY 17 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A GLN 4.1 0.2 - - - -
10A TYR 3.3 12.6 - - - -
13A ASN* 3.0 23.8 + - - +
16A ASP* 1.3 82.1 - - - +
18A LEU* 1.3 61.7 + - - -
19A MET 3.3 2.7 - - - -
20A GLY 2.8 16.1 + - - -
21A LYS* 3.0 11.8 + - - +
401A VAL* 3.6 4.0 - - - -
406A LEU* 3.7 10.5 - - - -
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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
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10A TYR* 2.7 19.9 + - + +
11A TYR* 3.4 23.2 + - + +
17A GLY* 1.3 71.6 - - - -
19A MET* 1.3 63.0 + - - +
21A LYS* 3.0 4.9 + - + +
22A LEU* 2.9 53.0 + - + +
285A PHE* 3.6 20.9 - - + -
288A ALA* 4.9 2.7 - - + -
397A PHE* 3.7 44.2 - - + -
400A ARG* 4.5 17.7 - - + +
401A VAL* 3.4 17.2 - - + +
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Residues in contact with MET 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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11A TYR 2.9 20.1 + - - +
12A THR* 3.9 19.5 - - - +
13A ASN 4.4 0.2 - - - +
14A ARG* 4.8 4.0 - - + -
17A GLY 3.3 0.4 - - - -
18A LEU* 1.3 74.8 - - - +
20A GLY* 1.3 63.1 + - - +
22A LEU* 4.4 2.5 - - - +
23A VAL* 3.1 53.0 + - + +
281A LYS* 4.0 33.4 - - + +
284A ARG* 3.7 28.5 - - - +
285A PHE* 3.6 24.9 - - + -
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Residues in contact with GLY 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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13A ASN 3.2 4.8 + - - -
14A ARG* 3.1 33.2 - - - +
15A ASN 4.0 6.9 - - - +
17A GLY 2.8 10.6 + - - -
19A MET* 1.3 80.2 - - - +
21A LYS* 1.3 63.4 + - - +
23A VAL* 4.3 9.8 - - - +
122A ARG* 5.3 1.2 - - - -
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Residues in contact with LYS 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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15A ASN 4.3 11.6 + - - +
16A ASP* 3.9 23.5 + - - +
17A GLY 3.0 14.6 + - - +
18A LEU* 3.0 10.1 + - + +
20A GLY* 1.3 81.3 - - - +
22A LEU* 1.3 59.6 + - - +
122A ARG* 3.3 29.8 + - - +
400A ARG* 3.3 58.5 + - + +
401A VAL* 4.3 4.0 - - + +
402A THR* 5.1 7.4 + - - +
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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
----------------------------------------------------------
18A LEU* 2.9 40.7 + - + +
19A MET* 4.1 4.5 - - - +
21A LYS* 1.3 79.5 - - - +
23A VAL* 1.3 64.1 + - - +
24A LEU 3.3 1.2 + - - -
121A ASN* 3.4 27.1 - - + +
122A ARG* 2.8 26.5 + - - +
284A ARG* 3.9 21.1 - - + +
285A PHE* 3.9 14.1 - - + -
288A ALA* 3.7 23.3 - - + -
400A ARG* 3.4 37.9 - - - +
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Residues in contact with VAL 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 MET* 3.1 44.6 + - + +
20A GLY* 4.3 7.6 - - - +
21A LYS 3.6 0.2 - - - -
22A LEU* 1.3 76.0 - - - +
24A LEU* 1.3 75.3 + - + +
25A THR* 3.5 1.9 + - - +
122A ARG* 3.6 8.7 - - - -
284A ARG* 3.9 23.8 - - - +
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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