Contacts of the strand formed by residues 491 - 501 (chain A) in PDB entry 6T2C
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 491 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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293A LEU* 3.4 6.2 - - - +
294A ASN* 2.9 45.1 + - - +
295A PRO* 4.9 9.6 - - + +
483A LYS* 4.2 23.2 - - - +
484A CYS 3.6 8.5 - - - +
485A ARG* 4.5 12.6 - - + +
489A GLY 4.7 0.4 - - - +
490A GLN* 1.3 79.4 - - - +
492A ARG* 1.3 61.1 + - - +
493A THR* 5.8 0.8 + - - -
567B ASN* 3.5 32.7 + - - +
568B LEU* 4.9 7.3 - - - +
34V U 3.3 60.3 + - - +
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Residues in contact with ARG 492 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291A SER* 3.9 21.2 - - - -
292A VAL 3.3 13.0 - - - +
293A LEU* 3.4 35.3 - - + +
294A ASN 4.5 0.4 - - - +
295A PRO* 5.1 1.3 - - - +
415A SER* 5.5 3.0 + - - -
483A LYS* 3.5 4.5 - - - +
484A CYS* 2.9 47.7 + - - +
485A ARG* 5.4 1.5 - - - -
486A ASP* 3.0 34.7 + - - +
490A GLN 4.7 1.6 - - - +
491A ARG* 1.3 79.9 - - - +
493A THR* 1.3 64.4 + - - +
494A ASN* 3.5 24.5 + - - +
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Residues in contact with THR 493 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290A LEU 3.7 1.7 - - - +
291A SER* 3.3 2.8 - - - -
292A VAL* 2.9 38.2 + - - -
295A PRO* 3.9 21.7 - - - +
306A ASP* 4.4 19.1 + - + +
310A CYS* 3.8 17.9 - - - -
481A ILE* 3.8 25.4 - - + -
482A THR 3.7 3.1 - - - +
483A LYS* 4.1 15.3 - - + +
491A ARG* 5.8 1.0 + - - -
492A ARG* 1.3 73.7 + - - +
494A ASN* 1.3 63.0 + - - +
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Residues in contact with ASN 494 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289A LYS* 3.9 32.0 + - + +
290A LEU 3.5 4.9 - - - -
291A SER* 3.0 20.5 + - - +
417A TRP* 4.2 4.1 - - - -
480A ILE 3.9 0.2 - - - +
481A ILE* 3.4 5.5 - - - +
482A THR* 2.9 57.9 + - - +
484A CYS* 3.2 30.3 - - - -
492A ARG* 3.5 15.2 + - - +
493A THR* 1.3 76.1 - - - +
495A LEU* 1.3 59.4 + - - +
496A TYR* 4.3 2.2 - - + -
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Residues in contact with LEU 495 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288A MET 3.9 0.5 - - - +
289A LYS* 3.2 4.6 - - - -
290A LEU* 2.9 35.5 + - + +
307A ALA* 3.8 22.4 - - + +
310A CYS* 3.7 32.1 - - + -
311A LEU* 4.5 8.3 - - + +
479A PRO* 4.4 6.1 - - + -
480A ILE 3.4 19.1 - - - +
481A ILE* 3.7 18.6 - - + -
494A ASN* 1.3 74.5 - - - +
496A TYR* 1.3 63.9 + - - +
497A GLY 3.6 23.6 - - - +
498A PHE* 4.4 13.0 - - + -
520A PHE* 4.4 12.3 - - + -
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Residues in contact with TYR 496 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287A ALA* 4.1 14.5 - - + +
288A MET 3.8 18.0 - - - +
289A LYS* 3.8 26.4 - - + +
417A TRP* 4.1 1.9 - - - -
452A GLU* 2.4 35.9 + - - +
456A LYS* 3.8 28.9 - - - -
480A ILE* 2.9 39.9 + - + -
482A THR* 3.2 40.0 + - + -
494A ASN* 4.3 4.3 - - + -
495A LEU* 1.3 75.3 - - - +
497A GLY* 1.3 59.4 + - - +
519A GLU* 3.8 10.9 - - - +
520A PHE* 3.2 32.2 + - - +
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Residues in contact with GLY 497 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479A PRO* 3.6 1.0 - - - +
480A ILE* 2.8 34.1 + - - +
495A LEU* 3.6 9.6 - - - +
496A TYR* 1.3 80.3 - - - +
498A PHE* 1.3 66.5 + - - -
518A LEU 3.3 13.5 - - - -
519A GLU* 4.2 2.5 - - - -
520A PHE* 4.1 12.6 - - - -
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Residues in contact with PHE 498 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304A MET* 4.9 3.1 - - + -
307A ALA* 4.0 23.3 - - + -
311A LEU* 3.6 22.7 - - + -
338A TRP* 4.8 10.3 - + - -
341A LEU* 4.0 28.9 - - + -
345A ILE* 3.6 27.6 - - + -
477A VAL* 4.2 16.2 - - + -
478A ILE 3.4 3.8 - - - +
479A PRO* 4.1 13.5 - - + -
480A ILE* 4.6 1.4 - - - +
495A LEU* 4.4 10.8 - - + -
497A GLY* 1.3 80.5 - - - -
499A ILE* 1.3 68.5 + - - +
500A ILE* 4.3 0.7 - - + -
517A SER* 3.6 0.2 - - - -
518A LEU* 2.9 40.4 + - + +
520A PHE* 4.0 23.6 - + - -
558A LEU* 6.4 0.2 - - + -
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Residues in contact with ILE 499 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A LYS 5.6 2.7 - - - +
460A ILE* 3.8 31.6 - - + -
464A LEU* 4.9 8.7 - - + -
476A GLN 3.6 0.7 - - - +
477A VAL* 4.6 0.2 - - - -
478A ILE* 2.5 64.4 + - + +
480A ILE* 4.0 24.5 - - + -
498A PHE* 1.3 80.0 - - - +
500A ILE* 1.3 64.6 + - - +
501A LYS 3.7 1.1 + - - +
515A PHE* 3.7 38.4 - - + -
516A ILE 3.3 2.9 - - - -
517A SER* 4.4 12.3 - - - -
519A GLU* 5.5 0.7 - - - +
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Residues in contact with ILE 500 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337A ILE* 4.1 21.5 - - + +
341A LEU* 4.3 13.9 - - + -
355A LEU* 3.8 30.5 - - + -
361A LEU* 4.1 18.8 - - + -
365A LEU* 3.8 4.9 - - + +
475A TYR* 4.4 9.4 - - + +
476A GLN 3.9 2.9 - - - +
477A VAL* 4.2 14.1 - - + +
499A ILE* 1.3 73.0 - - - +
501A LYS* 1.3 73.6 + - - +
515A PHE* 3.2 4.5 - - - -
516A ILE* 2.9 41.8 + - + +
518A LEU* 4.1 23.6 - - + -
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Residues in contact with LYS 501 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365A LEU* 3.3 14.8 - - - +
464A LEU* 3.7 25.6 - - + -
467A SER* 2.5 47.1 + - - -
468A SER* 3.8 17.7 - - - +
471A ALA 2.5 20.8 + - - -
472A MET* 4.2 0.8 - - - +
474A GLU 4.3 3.3 + - - -
475A TYR* 3.4 14.6 - - - -
476A GLN* 3.1 29.8 + - - +
478A ILE* 4.6 5.8 - - + -
499A ILE* 3.7 2.3 + - - -
500A ILE* 1.3 77.2 - - - +
502A GLY* 1.3 80.7 + - - +
504A SER* 3.9 7.4 + - - +
513A VAL* 4.2 9.6 - - + -
514A ASN 3.9 0.7 - - - -
515A PHE* 4.2 5.8 - - + -
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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