Contacts of the helix formed by residues 13 - 23 (chain A) in PDB entry 2YWD
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 ASP 13 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A GLY* 1.3 74.0 - - - -
14A PHE* 1.3 62.3 + - - +
15A ARG* 3.2 8.6 + - - +
16A GLU* 3.3 32.1 + - + +
17A HIS* 4.0 8.8 - - - -
46A PRO* 3.6 12.3 - - - +
47A GLY 3.1 24.5 + - - +
48A GLY* 4.7 4.2 - - - -
172A HIS* 5.7 4.0 - - + +
174A GLU* 4.9 4.9 - - - +
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Residues in contact with PHE 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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7A VAL* 3.4 27.5 - - + +
8A LEU 3.5 10.8 - - - +
9A ALA* 3.6 35.0 - - + -
10A LEU 5.4 0.2 - - - -
11A GLN* 4.3 8.7 - - - -
12A GLY 3.3 18.4 - - - -
13A ASP* 1.3 74.4 - - - +
15A ARG* 1.3 89.3 + - + +
17A HIS* 3.1 5.6 + - - +
18A LYS* 3.1 34.9 + - + +
30A GLU* 4.0 20.4 - - + -
32A ARG* 3.8 15.0 - - - -
46A PRO* 3.9 5.7 - - + +
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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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12A GLY 4.9 0.6 + - - +
13A ASP* 3.2 7.0 + - - -
14A PHE* 1.3 93.6 - - + +
16A GLU* 1.3 89.4 + - - +
18A LYS* 3.1 11.2 + - - +
19A GLU* 3.0 46.0 + - + +
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Residues in contact with GLU 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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13A ASP* 3.3 35.4 - - + +
14A PHE 3.3 0.4 - - - -
15A ARG* 1.3 109.7 + - - +
17A HIS* 1.3 58.1 + - - +
19A GLU* 3.5 15.0 + - - +
20A ALA* 3.0 27.4 + - - +
174A GLU* 3.5 31.3 - - + +
175A LEU* 3.9 23.3 - - + +
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Residues in contact with HIS 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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7A VAL* 4.0 17.5 - - + -
13A ASP 4.0 3.1 - - - -
14A PHE 3.1 8.9 + - - +
16A GLU* 1.3 76.9 - - - +
18A LYS* 1.3 61.0 + - - +
20A ALA* 3.2 2.3 + - - +
21A LEU* 2.8 36.9 + - - +
44A ILE* 3.7 20.4 - - + +
46A PRO* 3.7 28.3 - - + -
78A PHE* 5.0 1.3 - + - -
80A THR* 2.9 37.2 + - + -
174A GLU* 3.4 34.0 + - + +
182A HIS* 3.0 30.2 + + - -
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Residues in contact with LYS 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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7A VAL* 4.3 8.5 - - + -
14A PHE* 3.1 21.9 + - + +
15A ARG* 3.1 10.3 + - - +
17A HIS* 1.3 76.9 - - - +
19A GLU* 1.3 64.6 + - + +
21A LEU* 3.3 3.6 + - - +
22A LYS* 3.2 29.5 + - - +
26A ILE 4.6 1.2 - - - +
27A GLU* 5.2 6.5 + - - -
28A ALA* 3.6 47.0 + - + +
30A GLU* 3.3 40.6 - - + +
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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* 3.0 43.0 + - + +
16A GLU* 3.7 17.4 - - - +
18A LYS* 1.3 76.1 - - + +
20A ALA* 1.3 64.7 + - - +
22A LYS* 3.2 45.0 + - - +
23A ARG* 3.9 15.8 + - - +
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Residues in contact with ALA 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 GLU 3.0 17.9 + - - +
17A HIS* 3.2 5.6 + - - +
19A GLU* 1.3 76.5 - - - +
21A LEU* 1.3 62.0 + - - +
23A ARG* 3.2 35.9 + - - +
24A LEU* 4.1 2.9 + - - +
173A PRO 5.4 0.2 - - - +
174A GLU* 4.3 10.8 - - - +
176A THR 5.3 2.2 - - - +
178A ASP 6.0 0.7 - - - +
179A PRO* 4.2 11.5 - - + +
182A HIS* 3.8 31.8 - - + +
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Residues in contact with LEU 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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5A VAL* 3.8 26.2 - - + -
7A VAL* 3.9 13.2 - - + -
17A HIS 2.8 19.5 + - - +
18A LYS 3.6 5.2 - - - +
19A GLU 3.2 0.2 - - - -
20A ALA* 1.3 75.8 - - - +
22A LYS* 1.3 65.1 + - - +
24A LEU* 2.9 30.5 + - + +
26A ILE* 3.1 31.1 + - + +
28A ALA* 3.6 26.0 - - + -
44A ILE* 3.9 10.5 - - + -
182A HIS* 3.9 23.3 - - + -
185A PHE* 6.3 0.2 - - + -
186A LEU* 4.4 11.9 - - + -
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Residues in contact with LYS 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 LYS* 3.2 16.0 + - - +
19A GLU* 3.2 39.7 + - - +
21A LEU* 1.3 77.4 - - - +
23A ARG* 1.3 58.5 + - + +
24A LEU 3.0 0.2 - - - -
25A GLY* 2.8 21.5 + - - -
26A ILE 3.5 10.3 - - - +
27A GLU* 4.0 21.3 - - - +
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Residues in contact with ARG 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* 3.9 10.2 + - - +
20A ALA* 3.5 31.4 - - - +
21A LEU 3.1 1.0 - - - -
22A LYS* 1.3 76.0 - - + +
24A LEU* 1.3 61.8 + - - +
25A GLY 3.3 1.1 + - - -
176A THR 4.3 4.4 + - - -
177A GLU* 2.9 69.0 + - - +
179A PRO* 4.0 19.1 - - + +
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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