Contacts of the strand formed by residues 393 - 398 (chain Q) in PDB entry 6GYK
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 TYR 393 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117Q HIS* 3.4 34.1 + + + -
118Q LEU 3.3 15.3 + - - +
119Q LEU* 3.8 1.6 - - + -
120Q LYS* 3.3 24.5 + - - +
141Q ARG* 5.2 4.1 + - - -
346Q GLU* 5.6 0.9 + - - -
350Q TRP* 3.4 38.2 - + - +
363Q GLY 4.9 0.2 - - - -
364Q SER* 3.2 26.2 - - - +
365Q TYR* 3.6 26.8 - + + -
366Q GLU* 4.6 1.8 - - - +
391Q LYS* 3.4 33.0 + - + +
392Q VAL* 1.3 84.4 - - - +
394Q LYS* 1.3 60.7 + - - +
395Q PHE* 3.9 17.4 + - + -
135R PHE* 5.2 0.2 - + - -
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Residues in contact with LYS 394 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120Q LYS* 3.3 41.7 - - + +
121Q PHE 2.7 29.6 + - - -
122Q GLN* 3.3 38.3 + - + +
362Q VAL 4.0 0.5 - - - +
363Q GLY* 3.2 2.2 - - - -
364Q SER* 2.9 39.0 + - - +
365Q TYR 5.5 0.2 - - - +
366Q GLU* 3.4 24.6 + - - +
393Q TYR* 1.3 70.3 - - - +
395Q PHE* 1.3 63.2 + - - +
396Q THR* 3.9 7.0 + - - +
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Residues in contact with PHE 395 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119Q LEU* 3.5 29.8 - - + -
120Q LYS 2.5 12.8 + - - +
121Q PHE* 3.2 26.7 - + + -
122Q GLN* 3.0 25.8 + - - +
139Q LEU* 3.6 17.9 - - + -
350Q TRP* 3.3 39.7 - + - -
352Q MET* 3.6 31.0 - - + -
361Q TRP* 3.7 32.5 - - + -
363Q GLY* 3.7 11.7 - - - -
393Q TYR* 4.3 11.0 - - + -
394Q LYS* 1.3 74.2 - - - +
396Q THR* 1.3 60.6 + - - +
135R PHE* 4.9 0.9 - + - -
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Residues in contact with THR 396 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290B GLY 5.5 5.3 + - - +
292B ILE* 5.1 14.8 - - + -
122Q GLN* 4.0 25.2 - - + +
361Q TRP* 3.3 4.0 - - - -
362Q VAL* 2.9 36.6 + - - +
364Q SER* 5.8 0.2 + - - -
394Q LYS* 4.2 8.5 + - - +
395Q PHE* 1.3 76.2 + - - +
397Q ALA* 1.3 74.9 + - - +
398Q ARG* 3.2 17.7 + - - +
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Residues in contact with ALA 397 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292B ILE* 6.0 1.0 - - - +
122Q GLN 4.3 2.8 + - - -
123Q SER* 4.0 6.7 - - - -
360Q THR 3.4 9.0 - - - +
361Q TRP* 3.3 38.7 - - + -
396Q THR* 1.3 79.6 - - - +
398Q ARG* 1.3 60.3 + - - +
399Q ASN 4.3 0.2 + - - -
400Q LYS* 3.4 38.1 - - + +
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Residues in contact with ARG 398 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292B ILE* 4.4 16.8 - - + +
326B ASP* 4.2 8.0 + - - +
327B ARG* 5.1 14.3 - - - +
328B GLU* 3.4 34.8 + - - -
360Q THR* 2.9 39.5 + - + +
362Q VAL* 3.3 44.6 + - + +
364Q SER* 5.9 0.8 + - - -
396Q THR* 3.2 18.8 + - - +
397Q ALA* 1.3 74.6 - - - +
399Q ASN* 1.3 80.7 + - + +
400Q LYS* 3.5 2.0 - - - +
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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