Contacts of the strand formed by residues 356 - 361 (chain K) in PDB entry 6D6Q
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 356 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287K VAL* 3.6 19.9 - - + +
288K HIS* 5.2 2.9 - - + +
289K GLU 5.6 0.9 + - - -
352K ASN 4.7 2.6 + - - -
353K TRP* 4.4 8.6 - - + -
354K ARG* 3.1 66.4 + - + +
355K PRO* 1.3 71.7 - - - +
357K CYS* 1.3 62.3 + - - +
373K PHE* 3.7 10.1 - - + -
375K PRO* 4.4 15.9 - - + -
377K ASP* 3.8 15.0 - - - -
380K ILE* 3.7 30.0 - - + +
383K ILE* 5.1 3.4 - - + -
399K ILE* 3.3 2.6 - - - -
400K VAL 2.9 33.3 + - - +
402K ILE* 3.6 35.2 - - + -
436K GLU* 3.9 2.5 - - - +
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Residues in contact with CYS 357 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355K PRO 4.8 3.1 - - - -
356K TYR* 1.3 72.9 - - - +
358K GLY* 1.3 59.3 + - - +
373K PHE* 3.7 1.6 - - - -
375K PRO* 3.4 5.5 - - - +
376K ALA* 3.1 23.8 + - + +
398K ILE 3.4 5.8 - - - +
399K ILE* 3.2 26.2 - - + -
432K VAL* 3.8 32.5 - - + -
435K LEU* 3.6 34.8 - - - -
436K GLU* 2.7 23.6 + - - +
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Residues in contact with GLY 358 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357K CYS* 1.3 76.0 - - - +
359K MET* 1.3 64.9 + - - -
373K PHE* 3.2 17.0 - - - -
374K THR 3.4 7.9 - - - -
375K PRO* 3.9 1.3 - - - -
376K ALA 4.2 2.9 - - - -
397K ARG* 3.2 11.7 - - - +
398K ILE 2.9 31.3 + - - -
919K GLN* 4.4 8.5 - - - -
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Residues in contact with MET 359 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358K GLY* 1.3 75.7 - - - +
360K LEU* 1.3 61.3 + - - +
361K SER* 3.8 1.1 - - - +
373K PHE* 2.8 21.5 - - - -
374K THR* 2.9 32.8 + - - +
395K GLY* 4.5 18.6 - - - +
396K ARG 5.0 3.8 - - - +
397K ARG* 4.2 11.0 - - + +
398K ILE* 4.8 3.4 - - - +
423K VAL* 3.6 26.5 - - + -
918K LEU* 4.1 25.8 - - + -
919K GLN* 2.9 42.4 - - - +
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Residues in contact with LEU 360 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359K MET* 1.3 73.5 - - - +
361K SER* 1.3 62.4 + - - +
362K LYS* 3.4 5.6 + - + +
371K HIS* 3.6 26.2 - - + -
372K LEU 3.3 17.9 - - - +
373K PHE* 4.7 2.9 - - + -
385K ILE* 3.6 23.1 - - + -
387K THR* 4.4 8.3 - - + -
390K ALA* 4.3 17.9 - - + -
393K LEU* 3.9 40.9 + - + +
394K GLU* 4.2 26.3 - - + +
395K GLY 6.0 0.4 - - - +
396K ARG 5.4 2.0 + - - -
398K ILE* 4.6 10.9 - - + +
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Residues in contact with SER 361 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359K MET* 3.7 3.3 + - - +
360K LEU* 1.3 70.4 - - - +
362K LYS* 1.3 61.9 + - - +
371K HIS* 4.0 0.7 - - - +
372K LEU* 2.5 53.7 + - - +
374K THR* 3.5 26.8 + - - +
382K ARG* 5.3 3.4 + - - -
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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