Contacts of the strand formed by residues 360 - 365 (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 THR 360 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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351Q VAL* 3.7 11.9 - - + -
352Q MET 3.6 2.7 - - - -
353Q GLU* 3.3 29.1 + - - +
358Q TYR* 4.6 12.5 - - - -
359Q ASN* 1.3 76.9 + - - +
361Q TRP* 1.3 73.6 + - - +
362Q VAL* 4.1 5.4 - - + -
397Q ALA* 3.4 3.8 - - - +
398Q ARG* 2.9 57.5 + - + +
399Q ASN* 4.8 6.9 + - + +
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Residues in contact with TRP 361 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121Q PHE* 3.4 53.8 - + + -
122Q GLN 4.2 2.7 - - - -
123Q SER* 3.2 26.7 - - - -
128Q ASN* 4.3 17.5 - - + -
133Q PHE* 3.3 38.3 - + - -
351Q VAL* 3.2 4.9 - - - -
352Q MET* 2.9 52.4 + - + +
359Q ASN* 4.3 7.1 - - - +
360Q THR* 1.3 77.7 + - - +
362Q VAL* 1.3 62.6 + - - +
395Q PHE* 3.7 11.7 - - + -
396Q THR 3.3 9.4 - - - -
397Q ALA* 3.3 39.2 - - + +
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Residues in contact with VAL 362 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142Q LYS* 5.7 4.3 - - + -
349Q PRO* 4.5 13.5 - - + -
350Q TRP 3.7 10.8 - - - +
351Q VAL* 3.6 24.9 - - + -
360Q THR* 4.1 5.4 - - + -
361Q TRP* 1.3 71.4 - - - +
363Q GLY* 1.3 68.5 + - - +
364Q SER* 4.9 3.6 + - - +
394Q LYS 4.0 1.0 - - - +
395Q PHE* 4.2 0.7 - - - -
396Q THR* 2.9 34.0 + - - +
398Q ARG* 3.3 46.8 + - - +
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Residues in contact with GLY 363 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349Q PRO* 3.4 24.9 - - - +
350Q TRP* 3.6 16.3 + - - +
362Q VAL* 1.3 76.5 - - - +
364Q SER* 1.3 64.7 + - - -
393Q TYR* 4.9 0.6 - - - -
394Q LYS 3.2 11.4 - - - -
395Q PHE* 3.7 28.5 - - - -
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Residues in contact with SER 364 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B ARG* 3.9 22.6 + - - -
349Q PRO* 5.4 3.5 - - - +
362Q VAL* 4.9 3.6 + - - +
363Q GLY* 1.3 76.4 + - - -
365Q TYR* 1.3 67.8 + - - +
393Q TYR* 3.2 11.7 - - - -
394Q LYS* 2.9 36.7 + - - +
398Q ARG* 5.9 0.9 + - - -
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Residues in contact with TYR 365 (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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368B GLU 5.1 5.8 - - - -
369B GLY* 4.7 15.6 - - - +
343Q ARG* 3.8 34.3 + - + -
364Q SER* 1.3 82.4 - - - +
366Q GLU* 1.3 70.7 + - - +
367Q ALA* 3.7 37.0 + - + -
370Q SER* 5.2 5.6 + - - -
390Q ASP 4.9 0.9 + - - -
391Q LYS* 3.3 51.8 - - + +
392Q VAL* 3.4 11.4 - - + -
393Q TYR* 3.6 24.1 - + + -
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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