Contacts of the strand formed by residues 14 - 21 (chain A) in PDB entry 2ERY
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 LYS 14 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A GLN* 3.2 9.7 + - + +
13A GLU* 1.3 78.0 - - - +
15A TYR* 1.3 76.8 + - - +
16A ARG* 5.6 6.5 - - + +
63A ARG* 3.3 26.7 - - + +
65A ASP* 3.1 29.6 - - - +
87A GLU* 3.6 10.5 - - - +
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Residues in contact with TYR 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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13A GLU* 2.6 44.6 + - + +
14A LYS* 1.3 82.9 - - - +
16A ARG* 1.3 58.4 + - - +
17A LEU* 3.4 19.9 + - + +
60A ARG* 4.5 0.9 + - - -
62A ALA* 4.3 11.0 - - + -
63A ARG 2.9 10.9 + - - +
64A LEU* 3.6 5.9 - - + -
65A ASP* 2.8 34.8 + - - +
87A GLU* 3.4 11.4 - - - -
172A VAL* 3.8 30.3 - - + -
175A ILE* 3.5 34.8 - - + -
176A ARG* 3.6 10.9 - - + +
179A GLN* 3.5 21.2 + - - -
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Residues in contact with ARG 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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14A LYS* 5.6 6.4 + - + +
15A TYR* 1.3 70.2 - - - +
17A LEU* 1.3 62.4 + - - +
18A VAL* 4.8 1.6 - - + -
65A ASP* 3.4 18.4 - - + +
85A THR* 2.7 53.3 + - - +
86A GLY* 3.8 3.8 - - - -
87A GLU* 2.8 66.2 + - - +
88A GLY 3.4 4.5 + - - -
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Residues in contact with LEU 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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15A TYR* 4.0 15.9 - - + +
16A ARG* 1.3 78.2 - - - +
18A VAL* 1.3 65.3 + - - +
19A VAL* 6.0 0.7 - - + -
64A LEU* 3.9 32.1 - - + -
65A ASP 2.7 12.8 + - - +
66A ILE* 3.3 13.2 - - + +
67A LEU* 2.9 25.3 + - - +
88A GLY 3.4 4.7 - - - +
90A LEU* 6.3 0.2 - - + -
168A PHE* 4.1 18.6 - - + +
171A LEU* 3.8 26.2 - - + -
172A VAL* 4.3 9.2 - - + -
175A ILE* 3.4 33.0 - - + -
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Residues in contact with VAL 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ARG* 4.6 2.5 - - + +
17A LEU* 1.3 80.5 - - - +
19A VAL* 1.3 63.1 + - - +
20A VAL* 3.8 13.5 + - + -
67A LEU* 3.7 16.2 - - + -
69A THR* 3.6 25.8 - - + -
82A TYR* 3.8 24.2 - - + +
86A GLY* 4.0 26.5 - - - -
88A GLY 3.0 6.4 + - - +
89A PHE* 3.3 19.4 - - + +
90A LEU* 3.0 24.7 + - - +
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Residues in contact with VAL 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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17A LEU* 5.5 0.4 - - + -
18A VAL* 1.3 73.2 - - - +
20A VAL* 1.3 55.6 + - - +
27A LYS* 3.7 33.4 - - + +
30A LEU* 5.6 2.5 - - + -
31A THR* 3.9 11.0 - - - +
66A ILE* 3.8 26.7 - - + -
67A LEU 2.9 12.2 + - - +
68A ASP* 4.5 3.6 - - - -
69A THR* 2.6 35.5 + - - +
90A LEU* 3.7 13.0 - - + +
92A VAL* 3.8 21.8 - - + -
168A PHE* 4.1 17.9 - - + -
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Residues in contact with VAL 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 VAL* 3.8 19.7 - - + -
19A VAL* 1.3 78.6 - - - +
21A GLY* 1.3 58.9 + - - +
27A LYS* 3.6 4.7 - - - -
69A THR* 3.6 12.8 - - + +
82A TYR* 4.5 10.3 - - + +
83A MET* 5.0 5.8 - - + -
89A PHE* 4.4 12.3 - - + -
90A LEU 2.9 17.2 + - - +
91A LEU* 3.6 26.2 - - + -
92A VAL* 2.9 30.8 + - - +
107A PHE* 4.0 26.9 - - + -
111A ILE* 4.7 4.0 - - + -
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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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20A VAL* 1.3 78.1 - - - +
22A GLY* 1.3 69.7 + - - +
25A VAL* 4.4 0.7 - - - -
27A LYS* 3.2 15.6 + - - +
69A THR* 4.6 0.7 + - - -
92A VAL 3.4 15.5 - - - -
104A ILE* 5.3 0.2 - - - -
107A PHE* 3.5 29.8 - - - -
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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