Contacts of the helix formed by residues 11 - 21 (chain A) in PDB entry 2YWB
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 TYR 11 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A SER* 2.9 13.2 + - - +
10A GLN* 1.3 103.9 + - + +
12A THR* 1.3 63.8 + - - +
13A ARG 3.2 2.9 - - - -
14A LEU* 3.0 26.0 + - + +
15A ILE* 2.9 24.7 + - - +
100A TYR* 3.5 38.1 - + - -
123A TRP* 3.6 21.1 + + - -
164A HIS* 3.9 20.4 - + + -
166A GLU* 3.5 20.0 - - + +
167A VAL* 4.0 20.0 - - + +
169A HIS* 5.7 0.7 - - - -
457A ASP* 4.9 12.8 - - + -
459A MET* 4.9 5.8 - - - -
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Residues in contact with THR 12 (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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4A VAL* 3.8 18.6 - - + +
6A ASP* 2.6 46.8 + - + +
9A SER* 3.1 16.8 + - - -
10A GLN 3.4 0.8 - - - -
11A TYR* 1.3 77.1 - - - +
13A ARG* 1.3 62.5 + - - +
15A ILE* 3.2 15.5 + - - +
16A ALA* 3.1 18.5 + - - +
28A ILE* 3.9 15.3 - - + -
49A SER* 3.3 13.2 + - - -
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Residues in contact with ARG 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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10A GLN 4.7 5.2 + - - +
11A TYR 3.2 0.4 - - - -
12A THR* 1.3 75.5 - - - +
14A LEU* 1.3 68.8 + - - +
16A ALA* 3.0 5.5 + - - +
17A ARG* 2.9 45.2 + - - +
28A ILE* 3.9 16.8 - - + +
319A PRO* 4.1 38.7 - - - +
322A ILE* 4.7 16.8 - - + -
358A PHE* 3.9 16.0 - - + -
457A ASP 5.4 0.2 + - - -
458A PHE* 3.9 23.2 + - - +
459A MET* 4.1 22.4 - - + +
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Residues in contact with LEU 14 (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 GLN 5.3 0.2 + - - -
11A TYR* 3.0 36.6 + - + +
13A ARG* 1.3 80.8 - - - +
15A ILE* 1.3 62.5 + - - +
17A ARG* 2.9 13.4 + - - +
18A ARG* 2.9 54.3 + - - +
166A GLU* 3.4 30.1 - - + +
167A VAL* 4.2 9.4 - - + -
457A ASP* 4.5 16.4 - - - +
458A PHE* 3.8 26.5 - - + -
459A MET* 6.3 1.8 - - - -
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Residues in contact with ILE 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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4A VAL* 4.0 18.6 - - + -
9A SER* 5.6 0.4 - - - +
11A TYR* 2.9 19.3 + - + +
12A THR* 3.4 8.7 - - - +
13A ARG 3.2 0.2 - - - -
14A LEU* 1.3 74.7 - - - +
16A ALA* 1.3 64.7 + - - +
18A ARG* 3.0 14.9 + - + +
19A LEU* 3.1 13.6 + - + +
47A ILE* 4.0 27.1 - - + -
49A SER* 3.8 30.7 - - - -
50A GLY 5.1 1.3 - - - +
77A ILE* 4.0 17.9 - - + -
166A GLU* 3.7 36.6 - - + +
177A LEU* 5.8 4.3 - - + -
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Residues in contact with ALA 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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4A VAL* 4.1 10.7 - - + +
12A THR 3.1 2.2 + - - +
13A ARG 3.0 10.6 + - - +
15A ILE* 1.3 81.3 - - - +
17A ARG* 1.3 57.4 + - - +
19A LEU 3.7 0.7 + - - -
20A ARG* 3.2 16.1 + - - +
26A SER* 2.7 30.9 + - - +
28A ILE* 3.8 33.7 - - + -
318A TYR* 4.8 3.4 - - + -
358A PHE* 4.0 11.7 - - + -
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Residues in contact with ARG 17 (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 ARG* 2.9 31.1 + - - +
14A LEU* 2.9 16.8 + - - +
16A ALA* 1.3 75.0 - - - +
18A ARG* 1.3 66.5 + - - +
20A ARG* 3.2 2.8 + - - +
21A GLU* 2.9 43.4 + - + +
319A PRO* 5.5 1.6 - - - +
358A PHE* 3.8 37.3 - - + +
359A LYS* 5.2 4.4 - - - +
360A ASP* 2.6 39.1 + - - +
458A PHE* 3.6 57.7 - - - +
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Residues in contact with ARG 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 LEU* 2.9 40.1 + - - +
15A ILE 3.0 5.3 + - - +
17A ARG* 1.3 76.8 - - - +
19A LEU* 1.3 57.5 + - + +
21A GLU* 3.1 27.6 + - - +
22A LEU* 3.0 34.4 + - - +
166A GLU* 2.8 42.2 + - + -
167A VAL 4.4 0.6 - - - -
168A ALA* 4.2 14.1 - - - +
174A MET* 3.4 33.8 - - + +
177A LEU* 3.7 15.0 - - + -
456A GLU 4.3 11.3 + - - -
458A PHE* 4.0 18.0 - - - -
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Residues in contact with LEU 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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2A VAL* 3.4 26.7 - - + -
4A VAL* 3.6 27.4 - - + -
15A ILE* 3.1 10.6 + - + +
16A ALA 3.9 1.1 - - - +
17A ARG 3.2 0.2 - - - -
18A ARG* 1.3 74.4 - - + +
20A ARG* 1.3 63.2 + - - +
22A LEU* 3.1 12.5 + - + -
24A ALA* 2.8 40.0 + - + +
26A SER* 3.6 15.5 - - - -
47A ILE* 3.7 24.0 - - + -
177A LEU* 5.6 7.2 - - + -
180A PHE* 5.9 0.2 - - + -
181A LEU* 3.9 31.2 - - + -
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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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16A ALA 3.2 12.7 + - - +
17A ARG* 3.2 5.6 + - + +
18A ARG 3.2 0.4 - - - -
19A LEU* 1.3 71.8 - - - +
21A GLU* 1.3 60.0 + - + +
22A LEU 2.9 4.5 - - - -
23A ARG* 2.8 27.0 + - - -
24A ALA 3.8 4.0 - - - -
25A PHE* 3.3 20.8 - - - +
26A SER* 2.8 51.0 + - - +
27A LEU* 4.5 0.2 - - - +
190A TRP* 3.9 35.0 - - + +
318A TYR* 3.8 19.8 - - - -
356A LEU 2.6 31.5 + - - -
357A LEU* 4.0 6.9 - - - +
358A PHE* 3.6 24.6 - - + +
361A GLU* 6.1 3.9 - - + +
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Residues in contact with GLU 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 ARG* 2.9 40.1 + - + +
18A ARG* 3.3 41.0 + - - +
20A ARG* 1.3 75.1 - - + +
22A LEU* 1.3 63.4 - - - +
23A ARG* 3.4 29.7 + - - +
174A MET* 4.0 11.2 - - + +
360A ASP* 3.9 15.2 - - - +
458A PHE* 4.9 3.5 - - - -
373C ASP* 4.3 18.5 + - - +
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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