Contacts of the strand formed by residues 15 - 20 (chain A) in PDB entry 6EKK
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 VAL 15 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A PHE* 3.7 6.6 - - - -
14A GLU* 1.3 82.4 - - - +
16A TYR* 1.3 70.2 + - - +
17A VAL* 4.3 7.2 - - + -
36A GLN* 4.7 1.8 - - + -
37A PHE 3.3 15.9 - - - +
41A TYR* 3.6 47.8 - - + +
46A VAL* 4.7 0.2 - - + -
47A LEU* 4.4 3.1 - - + -
50A LEU* 3.7 28.7 - - + +
98A CYS 4.0 0.7 - - - +
99A ILE* 3.6 1.2 - - - +
100A LEU* 2.9 39.3 + - + +
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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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13A PHE* 4.1 4.2 - - + -
15A VAL* 1.3 74.9 - - - +
17A VAL* 1.3 79.8 + - - +
18A GLU* 4.5 5.9 - - + +
35A ARG* 5.3 1.1 - - - -
36A GLN* 3.2 6.7 - - - +
37A PHE* 2.7 40.3 + - + +
97A PHE* 3.2 28.5 - + + -
98A CYS 3.3 17.3 - - - -
99A ILE* 4.3 8.5 - - + +
113A LEU* 3.9 18.6 - - + -
116A LEU* 3.7 30.6 - - + +
120A THR* 4.1 1.6 + - - -
128A TRP* 3.4 46.0 + + - -
132A LEU* 3.8 23.6 - - + -
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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
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15A VAL* 4.3 3.4 - - + +
16A TYR* 1.3 89.0 - - - +
18A GLU* 1.3 58.7 + - - +
19A VAL* 3.7 23.6 - - + -
33A VAL* 4.2 15.0 - - + -
35A ARG 3.4 5.4 - - - +
36A GLN* 4.2 3.8 - - + -
47A LEU* 3.7 29.6 - - + -
50A LEU* 4.0 26.7 - - + -
96A CYS 3.8 0.3 - - - +
97A PHE* 3.5 3.1 - - - -
98A CYS* 2.8 55.6 + - + +
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Residues in contact with GLU 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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16A TYR* 4.5 5.9 - - + +
17A VAL* 1.3 72.6 - - - +
19A VAL* 1.3 55.7 + - - +
33A VAL* 3.6 2.6 - - - -
34A GLN* 2.6 39.2 + - + -
35A ARG* 2.9 30.5 + - + +
95A SER* 6.4 0.9 - - - -
96A CYS 3.5 4.5 - - - -
97A PHE* 4.2 23.6 - - + +
120A THR* 5.8 2.5 - - + +
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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 VAL* 3.7 26.2 - - + -
18A GLU* 1.3 78.6 - - - +
20A ALA* 1.3 64.3 + - - +
31A PRO* 3.8 15.3 - - + -
32A GLU 3.4 15.7 - - - +
33A VAL* 4.4 11.7 - - + -
50A LEU 5.0 0.2 - - - +
51A THR* 4.2 15.7 - - + +
54A CYS* 4.2 14.4 - - + -
55A PHE* 3.6 23.4 - - + -
95A SER* 3.1 5.5 - - - -
96A CYS 2.7 43.1 + - - +
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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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19A VAL* 1.3 75.7 - - - +
21A TYR* 1.3 69.9 + - - +
31A PRO* 3.5 2.7 - - - +
32A GLU* 2.9 32.9 + - - +
34A GLN* 3.6 27.9 + - + +
55A PHE* 4.7 1.8 - - - -
94A LYS 3.7 11.7 - - - +
95A SER* 3.9 9.4 - - - -
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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