Contacts of the strand formed by residues 413 - 422 (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 ASN 413 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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370K ARG* 4.2 7.9 + - - +
383K ILE* 4.2 1.1 - - - -
384K ARG* 2.9 52.5 + - - +
402K ILE* 4.0 0.8 - - - -
403K ASP* 2.8 40.4 + - + +
404K GLY* 3.2 10.9 + - - +
406K PRO* 3.9 21.8 - - - +
412K PRO* 1.3 75.5 - - - +
414K GLY* 1.3 54.2 + - - +
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Residues in contact with GLY 414 (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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72A THR* 5.1 4.0 + - - +
125A ALA* 5.7 0.3 - - - +
383K ILE* 3.5 23.2 - - - +
384K ARG 3.8 4.9 + - - +
385K ILE* 3.7 15.1 - - - +
386K GLU* 4.9 2.9 + - - +
400K VAL* 4.2 0.9 - - - -
401K ALA 3.1 13.9 - - - -
402K ILE* 4.1 3.4 - - - -
403K ASP* 3.8 6.9 - - - +
413K ASN* 1.3 75.0 - - - +
415K HIS* 1.3 64.4 + - - +
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Residues in contact with HIS 415 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A THR* 4.0 24.2 - - + -
122A CYS* 3.7 34.0 + - + -
123A VAL* 3.8 18.9 + - - -
125A ALA* 4.7 0.4 - - + -
385K ILE* 4.3 4.9 - - - -
386K GLU 5.9 0.2 - - - +
400K VAL* 3.2 9.8 - - - +
401K ALA* 2.9 46.4 + - + +
403K ASP* 2.6 38.8 + - - +
414K GLY* 1.3 75.0 - - - +
416K PHE* 1.3 73.5 + - - +
417K VAL* 3.4 17.1 - - + +
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Residues in contact with PHE 416 (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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72A THR* 5.7 0.6 - - - +
117A ASP* 3.4 25.8 - - - -
119A GLU* 3.6 32.9 - - + +
120A SER* 4.4 8.0 - - - +
385K ILE* 4.9 14.3 - - + +
387K THR* 5.2 5.6 - - + -
389K GLN* 5.3 4.0 - - - -
393K LEU* 4.3 17.5 - - + -
398K ILE* 3.5 38.4 - - + -
399K ILE 3.9 4.5 - - - -
400K VAL* 4.3 4.8 - - - +
415K HIS* 1.3 81.5 - - - +
417K VAL* 1.3 67.0 + - - +
418K ARG* 3.1 44.0 - - - -
419K ASN* 3.1 12.8 - - + -
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Residues in contact with VAL 417 (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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120A SER* 3.5 28.3 - - - +
122A CYS 4.4 7.6 - - - +
162A ARG* 6.0 0.3 + - - -
355K PRO* 4.8 7.4 - - + -
399K ILE* 3.0 39.7 + - + +
400K VAL* 4.6 1.1 - - - +
401K ALA* 4.2 8.5 - - + -
415K HIS* 3.4 29.4 - - + +
416K PHE* 1.3 85.6 - - - +
418K ARG* 1.3 70.7 + - + +
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Residues in contact with ARG 418 (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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120A SER* 5.1 1.3 - - - -
398K ILE* 3.6 0.7 - - - -
399K ILE* 3.1 46.8 + - + +
416K PHE* 3.1 17.0 - - - -
417K VAL* 1.3 84.9 - - + +
419K ASN* 1.3 72.5 + - - +
420K LEU* 3.9 23.3 - - + +
431K GLU* 4.5 12.5 + - - -
435K LEU* 4.6 11.5 - - - +
441K HIS* 5.7 6.1 + - - -
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Residues in contact with ASN 419 (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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392K THR* 6.0 0.2 - - - -
393K LEU* 3.6 19.3 - - + +
396K ARG* 3.1 54.3 + - - +
397K ARG 2.9 15.4 - - - +
398K ILE* 4.3 1.6 - - - -
416K PHE* 3.1 17.9 - - + -
418K ARG* 1.3 90.6 + - - +
420K LEU* 1.3 81.0 + - - +
421K GLY 3.3 7.3 + - - -
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Residues in contact with LEU 420 (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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396K ARG* 4.2 7.2 + - - -
397K ARG 3.2 13.9 + - - +
398K ILE 4.3 0.7 - - - -
399K ILE* 3.6 28.0 - - + -
418K ARG* 3.9 25.4 - - + +
419K ASN* 1.3 93.1 + - - +
421K GLY* 1.3 57.3 + - - +
427K GLU 5.7 0.3 - - - +
428K THR* 3.8 15.1 + - + +
431K GLU* 3.9 30.7 - - + +
432K VAL* 3.6 30.1 - - + -
435K LEU* 4.3 12.3 - - + -
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Residues in contact with GLY 421 (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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396K ARG* 3.8 19.3 - - - -
397K ARG 3.2 18.2 + - - -
419K ASN* 3.3 4.2 + - - -
420K LEU* 1.3 81.1 - - - +
422K ASP* 1.3 70.4 + - - +
425K GLU* 4.6 4.9 - - - -
428K THR* 3.3 17.3 + - - +
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Residues in contact with ASP 422 (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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395K GLY 3.2 15.7 - - - +
396K ARG* 3.7 13.1 - - + +
421K GLY* 1.3 76.1 - - - +
423K VAL* 1.3 71.6 + - - +
425K GLU* 2.9 34.8 + - - +
428K THR* 3.6 8.5 + - - -
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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