Contacts of the strand formed by residues 467 - 475 (chain C) in PDB entry 6KQH
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 ILE 467 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140C ILE* 5.8 0.4 - - + -
328C LEU* 4.9 11.6 + - + +
331C ARG 5.4 1.7 + - - +
333C ILE* 3.7 32.8 - - + -
410C ILE* 4.0 7.0 - - + -
437C ARG* 3.2 41.6 + - + -
438C ILE* 3.8 29.6 - - + -
455C LEU* 3.7 30.1 - - + -
459C ALA* 3.7 8.5 - - + -
460C ARG 3.2 11.0 - - - +
461C VAL* 4.5 5.8 - - + -
466C PHE* 1.3 74.0 - - - +
468C ARG* 1.3 63.1 + - - +
486C MET 4.0 1.4 - - - +
487C THR* 4.2 5.4 - - - -
488C ALA 4.7 0.5 + - - -
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Residues in contact with ARG 468 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437C ARG* 4.6 2.7 - - - -
459C ALA* 3.4 5.5 - - - +
460C ARG* 2.6 38.1 + - + +
461C VAL 5.5 0.4 - - - -
462C ASP* 3.0 50.5 + - - +
466C PHE 4.1 1.3 - - - +
467C ILE* 1.3 75.2 - - - +
469C THR* 1.3 59.3 + - - +
485C TYR* 3.3 41.6 + - + +
486C MET* 2.9 21.1 - - - +
487C THR* 3.4 23.1 + - + +
490C GLU* 5.7 5.5 - - - +
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Residues in contact with THR 469 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435C TYR 4.2 2.9 - - - +
436C GLY* 3.2 27.0 + - - -
437C ARG* 3.7 15.7 - - - +
468C ARG* 1.3 74.3 - - - +
470C PRO* 1.3 65.1 - - - +
471C TYR* 3.5 31.7 - - + +
484C VAL 3.6 0.5 - - - +
485C TYR* 3.4 3.9 - - - -
486C MET 2.9 26.7 + - - -
491C GLU* 3.6 11.9 - - - +
538C GLN* 2.4 34.7 + - - -
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Residues in contact with PRO 470 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C ILE* 3.9 1.8 - - + -
458C TYR* 3.5 32.5 - - + +
469C THR* 1.3 93.6 - - - +
471C TYR* 1.3 68.7 + - - +
483C VAL* 3.9 12.6 - - + -
484C VAL 3.5 6.1 - - - +
485C TYR* 3.4 34.8 - - + +
534C VAL* 3.8 19.4 - - + +
538C GLN* 3.1 27.6 + - - +
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Residues in contact with TYR 471 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435C TYR* 3.6 8.4 - + - -
469C THR* 3.5 24.9 - - + +
470C PRO* 1.3 78.8 - - - +
472C ARG* 1.3 63.4 + - - +
483C VAL* 3.0 7.4 - - - +
484C VAL 2.9 33.8 + - - +
486C MET* 3.8 22.9 - - + -
491C GLU* 2.5 34.1 + - + -
496C ILE* 3.5 28.0 - - + -
516C ARG* 2.7 19.2 + - - -
531C PHE* 4.1 19.1 - - + -
532C MET 3.7 3.6 - - - +
533C ASP* 3.0 35.0 - - - -
534C VAL* 4.2 4.9 - - - -
538C GLN* 4.1 4.7 - - - -
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Residues in contact with ARG 472 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C ILE* 5.5 4.6 - - - +
10C ARG* 4.0 23.8 + - - +
12C VAL* 3.3 37.7 - - + +
471C TYR* 1.3 77.1 - - - +
473C ARG* 1.3 61.9 + - - +
474C VAL* 3.8 0.5 - - - +
479C VAL* 3.4 28.6 + - + +
480C THR 3.2 21.0 + - - +
481C ASP* 4.3 1.2 + - - -
482C GLU 3.6 6.1 - - - +
483C VAL* 4.9 4.5 - - + -
499C ALA* 5.4 0.6 + - - +
503C LEU* 4.1 11.5 - - - +
506C ASN* 5.4 1.6 - - - +
531C PHE* 3.0 11.8 - - - -
532C MET* 2.8 64.2 + - + +
533C ASP 4.2 10.7 + - - -
534C VAL* 4.4 19.5 + - + +
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Residues in contact with ARG 473 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471C TYR 4.2 0.4 + - - -
472C ARG* 1.3 72.7 - - - +
474C VAL* 1.3 65.5 + - - +
475C VAL* 3.8 24.2 - - + -
479C VAL* 3.7 0.2 - - - -
480C THR* 2.9 44.9 + - + +
482C GLU* 2.8 49.8 + - + +
484C VAL* 4.1 11.1 - - + +
494C TYR* 5.8 1.2 + - - -
530C GLU 4.7 2.2 - - - -
531C PHE* 3.5 36.8 - - + -
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Residues in contact with VAL 474 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472C ARG 3.8 9.2 - - - +
473C ARG* 1.3 80.7 - - - +
475C VAL* 1.3 64.4 + - - +
476C GLY 4.2 0.7 + - - -
477C GLY* 4.0 22.7 - - - +
478C VAL 3.2 10.3 - - - +
479C VAL* 4.0 15.9 - - + +
508C ILE* 4.2 4.7 - - + -
529C VAL* 3.3 48.0 - - + +
530C GLU* 2.9 25.6 + - - +
531C PHE 3.9 8.1 - - - -
532C MET* 3.9 11.4 - - + -
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Residues in contact with VAL 475 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473C ARG* 3.8 26.0 - - + -
474C VAL* 1.3 75.5 - - - +
476C GLY* 1.3 68.9 + - - +
477C GLY 3.3 0.7 - - - -
478C VAL* 3.0 28.6 + - + +
480C THR* 4.9 6.7 - - + +
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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