Contacts of the strand formed by residues 396 - 404 (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 ARG 396 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358K GLY 4.5 0.9 - - - +
359K MET* 5.0 6.5 - - - +
360K LEU* 5.4 0.7 + - - +
392K THR* 3.4 26.3 + - - +
393K LEU 2.7 22.2 + - - +
394K GLU 5.2 0.9 - - - +
395K GLY* 1.3 77.1 - - - +
397K ARG* 1.3 66.6 + - - +
398K ILE* 3.3 12.0 + - - +
419K ASN* 3.1 41.6 + - - +
420K LEU 4.2 5.7 + - - -
421K GLY* 3.5 22.9 - - - +
422K ASP* 3.7 14.9 - - + +
423K VAL* 5.0 0.4 - - - -
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Residues in contact with ARG 397 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358K GLY* 3.2 12.5 - - - +
359K MET* 4.2 1.3 - - + -
376K ALA* 4.5 3.4 - - - +
395K GLY 4.2 1.0 + - - -
396K ARG* 1.3 68.7 - - - +
398K ILE* 1.3 61.2 + - - +
419K ASN* 2.9 17.7 - - - +
420K LEU* 3.2 15.2 + - + +
421K GLY 3.2 5.3 + - - -
423K VAL* 4.0 15.8 - - + +
428K THR* 3.8 19.5 - - + -
429K GLU* 2.3 44.1 + - - -
432K VAL* 3.5 42.2 - - + +
918K LEU 3.9 14.5 + - - -
919K GLN* 2.6 55.0 + - - +
920K HIS 5.0 2.2 - - - +
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Residues in contact with ILE 398 (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* 3.4 1.2 - - - +
358K GLY 2.9 31.6 + - - +
359K MET* 4.8 2.5 - - - -
360K LEU* 4.6 11.9 - - + -
373K PHE* 3.6 23.6 - - + -
385K ILE* 4.6 11.9 - - + -
393K LEU* 3.9 24.0 - - + -
396K ARG 3.3 15.5 + - - +
397K ARG* 1.3 76.1 - - - +
399K ILE* 1.3 70.3 + - - +
400K VAL* 3.6 23.8 - - + -
416K PHE* 3.5 33.2 - - + -
418K ARG 3.6 5.8 - - - -
419K ASN* 4.2 3.8 - - - +
420K LEU* 4.3 0.4 - - - +
432K VAL* 6.0 0.2 - - - +
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Residues in contact with ILE 399 (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* 4.1 19.5 - - + +
356K TYR 3.3 11.2 - - - +
357K CYS* 3.2 28.9 - - - -
358K GLY 4.8 0.2 - - - +
398K ILE* 1.3 82.0 - - - +
400K VAL* 1.3 64.9 + - - +
416K PHE* 3.9 1.9 - - - -
417K VAL* 3.0 46.7 + - + +
418K ARG* 3.1 31.4 + - + +
420K LEU* 3.6 15.7 - - + -
435K LEU* 4.3 14.4 - - + -
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Residues in contact with VAL 400 (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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354K ARG 4.1 0.9 - - - +
355K PRO* 3.3 3.9 - - - +
356K TYR* 2.9 32.8 + - - +
373K PHE* 4.0 26.0 - - + -
383K ILE* 4.4 12.2 - - + +
385K ILE* 3.8 18.2 - - + -
398K ILE* 3.6 25.8 - - + -
399K ILE* 1.3 80.5 - - - +
401K ALA* 1.3 68.5 + - - +
402K ILE* 4.3 0.5 + - - +
414K GLY* 4.2 3.6 - - - -
415K HIS 3.2 29.6 - - - +
416K PHE* 4.3 5.2 - - - +
417K VAL* 4.7 1.1 - - - +
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Residues in contact with ALA 401 (chain K).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167A VAL* 5.3 13.9 - - + -
354K ARG 4.8 2.2 - - - -
355K PRO* 4.6 13.5 - - + -
400K VAL* 1.3 75.9 - - - +
402K ILE* 1.3 66.6 + - - +
414K GLY* 3.1 1.7 - - - -
415K HIS* 2.9 58.4 + - + +
417K VAL* 4.2 8.2 - - + +
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Residues in contact with ILE 402 (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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169A GLY 5.3 2.3 - - - +
287K VAL* 5.2 9.4 - - + -
353K TRP* 3.3 50.9 - - + +
354K ARG 5.1 2.2 + - - -
356K TYR* 3.6 32.8 - - + -
380K ILE* 5.0 7.2 - - + -
381K PRO* 6.0 1.8 - - + -
383K ILE* 3.8 31.4 - - + -
400K VAL 5.4 0.2 - - - +
401K ALA* 1.3 75.2 - - - +
403K ASP* 1.3 72.2 + - - +
404K GLY 3.8 19.7 - - - +
412K PRO* 4.1 15.9 - - + -
413K ASN 4.0 4.0 - - - +
414K GLY* 4.1 1.3 - - - -
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Residues in contact with ASP 403 (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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123A VAL 4.8 1.9 - - - +
124A VAL* 4.9 1.6 - - - +
125A ALA* 3.0 33.1 + - + +
353K TRP* 3.8 9.9 - - - -
401K ALA 4.1 0.2 - - - -
402K ILE* 1.3 82.6 - - - +
404K GLY* 1.3 59.1 + - - +
413K ASN* 2.8 17.2 + - + +
414K GLY 3.8 8.5 - - - +
415K HIS* 2.6 41.2 + - - +
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Residues in contact with GLY 404 (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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351K ARG* 6.1 0.4 - - - -
353K TRP* 3.7 16.0 - - - -
402K ILE* 3.9 1.7 - - - +
403K ASP* 1.3 79.8 - - - +
405K TRP* 1.3 60.4 + - - +
406K PRO* 4.2 2.9 - - - -
412K PRO* 2.9 27.2 - - - +
413K ASN* 3.2 12.6 + - - -
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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