Contacts of the strand formed by residues 11 - 16 (chain A) in PDB entry 4EWS
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 ILE 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 ALA* 3.5 0.9 - - - +
10A GLY* 1.4 81.5 - - - +
12A VAL* 1.4 69.4 + - - +
206A LEU* 4.8 1.3 - - + -
213A VAL* 4.2 18.6 - - + -
215A ILE* 4.4 3.4 - - + -
232A HIS* 2.8 42.6 + - + +
234A GLY* 3.7 20.9 - - - -
264A TRP* 3.3 11.9 - - - +
265A PHE* 3.6 32.8 - - + -
269A VAL* 3.8 16.2 - - + -
503A DLP 6.3 0.2 - - + -
507A 0RP 3.3 37.9 - - - -
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Residues in contact with VAL 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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9A ALA* 4.0 9.0 - - + -
11A ILE* 1.4 78.8 - - - +
13A CYS* 1.3 64.4 + - - +
229A GLU* 3.7 24.7 - - + +
230A SER 3.6 7.2 - - - +
231A HIS* 3.9 13.7 - - + -
232A HIS* 4.5 0.2 - - - -
250A PHE* 3.5 49.1 - - + -
255A LEU* 4.4 4.0 - - + -
262A TYR 3.9 0.4 - - - +
263A PHE* 3.3 8.3 - - - -
264A TRP* 2.8 49.2 + - + +
507A 0RP 4.4 2.5 - - - -
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Residues in contact with CYS 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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12A VAL* 1.3 74.1 - - - +
14A ARG* 1.3 63.7 + - - +
15A ILE* 3.8 27.3 + - - -
229A GLU* 3.3 5.9 - - - +
230A SER* 3.0 46.0 + - - +
232A HIS* 4.0 3.1 - - - +
261A LEU* 5.5 1.1 - - - -
262A TYR 3.7 3.1 - - - -
263A PHE* 3.6 21.8 - - + -
507A 0RP 3.8 39.6 - - - -
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Residues in contact with ARG 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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13A CYS* 1.3 75.3 - - - +
15A ILE* 1.3 60.8 + - - +
16A THR* 4.0 6.4 + - + -
227A TYR* 3.3 55.0 + - + -
228A LEU 3.4 13.2 - - - +
229A GLU* 2.8 29.1 + - + -
252A PRO* 2.8 28.9 + - - +
255A LEU* 3.2 36.0 + - + +
256A GLY 2.8 30.9 + - - -
257A ASP* 4.8 1.2 - - - +
260A MET 3.9 0.3 - - - +
261A LEU* 3.4 6.2 - - - +
262A TYR* 2.7 47.3 + - + +
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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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13A CYS* 3.8 13.0 - - - -
14A ARG* 1.3 71.7 - - - +
16A THR* 1.3 63.4 + - - +
19A ALA* 3.7 15.9 - - + -
20A LEU* 4.6 7.0 - - + +
227A TYR* 3.5 0.7 - - - -
228A LEU* 2.7 46.2 + - + +
260A MET 3.6 4.3 - - - +
261A LEU* 3.8 17.7 - - + -
501A 2OB 3.6 46.4 - - + -
507A 0RP 3.4 48.7 - - + -
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Residues in contact with THR 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 ARG* 4.2 5.8 - - + +
15A ILE* 1.3 77.5 - - - +
17A LYS* 1.4 65.9 + - - +
18A PRO* 3.2 15.5 - - - +
19A ALA* 3.1 11.4 + - - +
20A LEU* 3.3 17.1 + - - +
226A SER 3.7 7.0 - - - +
227A TYR* 3.8 13.0 - - + -
257A ASP* 3.7 26.5 - - - -
259A ARG 2.5 29.1 + - - +
260A MET* 3.1 12.5 + - - +
262A TYR* 4.0 13.9 - - + -
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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