Contacts of the strand formed by residues 198 - 204 (chain A) in PDB entry 5JG8
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 198 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196A ALA 4.2 7.4 - - - +
197A PRO* 1.3 82.0 - - - +
199A SER* 1.3 70.0 + - - +
200A ARG* 4.0 9.4 + - + +
271A ASP* 4.5 5.0 - - - +
499A GLN* 4.2 19.1 - - + -
500A ILE 3.5 16.8 - - - +
502A GLY* 3.9 2.9 - - - -
512A LEU* 4.0 19.7 - - + -
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Residues in contact with SER 199 (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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198A VAL* 1.3 72.9 - - - +
200A ARG* 1.3 61.5 + - - +
201A ILE* 3.8 17.5 + - - +
271A ASP* 4.0 8.5 - - - +
272A MET* 4.8 0.5 - - - -
372A TYR* 3.0 35.0 + - - -
498A TYR 3.5 1.9 - - - +
500A ILE* 2.8 45.9 + - - +
501A ASP 4.5 2.9 - - - -
502A GLY* 3.6 14.1 - - - -
503A ASN 4.9 0.2 - - - -
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Residues in contact with ARG 200 (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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198A VAL* 4.0 9.1 + - + +
199A SER* 1.3 74.1 - - - +
201A ILE* 1.3 59.5 + - - +
202A LEU 4.3 0.2 - - - -
267A ALA* 3.0 30.5 + - - +
268A GLY 3.1 25.1 + - - +
269A PRO* 3.6 25.1 + - - +
270A PHE* 3.8 4.0 - - + -
271A ASP* 2.9 39.5 + - - +
272A MET 3.7 0.3 + - - -
497A VAL* 3.8 15.9 - - + +
498A TYR 3.4 5.6 - - - +
499A GLN* 2.8 40.2 - - + +
515A GLU* 4.0 10.9 + - - -
517A TYR* 4.7 0.8 + - - -
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Residues in contact with ILE 201 (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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199A SER* 3.8 16.2 - - - +
200A ARG* 1.3 78.9 - - - +
202A LEU* 1.3 68.4 + - - +
203A PHE 3.7 0.7 + - - -
270A PHE* 4.5 0.7 - - - -
272A MET* 3.4 23.3 - - + +
274A TYR* 3.3 57.0 - - + +
372A TYR* 6.1 0.7 - - + -
375A LEU* 6.2 1.1 - - + -
421A HIS* 4.5 3.8 - - + -
497A VAL* 3.4 6.5 - - - +
498A TYR* 2.9 40.0 + - + +
500A ILE* 3.1 35.7 - - + -
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Residues in contact with LEU 202 (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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201A ILE* 1.3 72.6 - - - +
203A PHE* 1.3 60.7 + - - +
204A LEU* 3.7 35.4 - - + -
264A LEU* 4.1 23.3 - - + -
270A PHE* 3.6 29.5 - - + -
272A MET 2.9 7.7 + - - -
273A VAL* 3.1 29.7 - - + +
274A TYR 2.8 26.5 + - - -
307A LEU* 4.2 6.3 - - + -
495A TYR* 3.8 18.4 - - + -
496A ARG 3.3 18.4 - - - +
497A VAL* 4.0 7.2 - - + -
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Residues in contact with PHE 203 (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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201A ILE* 3.7 1.0 + - + -
202A LEU* 1.3 71.0 - - - +
204A LEU* 1.3 62.5 + - - +
205A THR* 3.7 14.2 + - + +
274A TYR* 3.4 29.8 - + + -
276A THR* 2.9 29.4 - - - -
423A ILE* 5.3 3.4 - - + -
454A PHE* 3.4 34.1 - - + -
455A PHE 4.2 14.8 - - - -
480A PHE 5.3 0.4 - - - -
482A ALA* 3.3 34.9 - - + +
495A TYR* 3.9 4.5 - - - +
496A ARG* 2.9 37.8 + - + +
498A TYR* 3.7 28.5 - + + -
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Residues in contact with LEU 204 (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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202A LEU* 3.7 42.0 - - + -
203A PHE* 1.3 72.8 - - - +
205A THR* 1.3 62.9 + - - +
207A LEU* 4.2 20.4 - - + -
260A LEU* 4.2 18.4 - - + -
261A LEU* 4.4 17.9 - - + -
273A VAL* 4.1 10.5 - - + -
274A TYR 3.0 10.7 + - - +
275A TRP* 3.3 13.1 - - + -
276A THR* 3.0 23.4 + - - -
303A VAL* 4.7 17.5 - - + -
307A LEU* 5.4 0.4 - - + -
485A ALA* 5.9 2.2 - - + -
495A TYR* 3.8 19.5 - - + +
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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