Contacts of the helix formed by residues 488 - 503 (chain B) in PDB entry 3TQI
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 PRO 488 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439B TYR* 3.2 42.8 - - + +
486B ASP 4.5 1.6 - - - +
487B LEU* 1.3 90.3 - - + +
489B HIS* 1.3 65.9 + - - +
490B GLU* 4.4 8.5 - - + +
491B PHE* 3.0 20.9 + - + +
492B LEU* 3.0 15.3 + - - +
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Residues in contact with HIS 489 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A GLN* 6.0 0.9 - - - -
484A TRP* 3.0 69.9 + + - -
486A ASP* 3.3 48.1 + - + +
515A ASN* 5.9 0.4 - - - -
487B LEU 3.7 1.4 + - - -
488B PRO* 1.3 70.9 - - - +
490B GLU* 1.3 65.4 + - - +
492B LEU* 3.5 0.8 + - - -
493B SER* 2.9 44.5 + - - -
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Residues in contact with GLU 490 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488B PRO* 4.4 6.9 - - + +
489B HIS* 1.3 82.8 + - - +
491B PHE* 1.3 58.3 + - + +
493B SER* 3.7 4.7 + - - -
494B LYS* 3.2 24.8 + - - +
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Residues in contact with PHE 491 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430B PHE* 4.6 3.1 - + - -
433B GLU* 3.7 12.3 - - + -
434B LEU* 3.5 54.7 - - + -
437B SER* 3.6 24.0 - - - -
439B TYR* 3.9 16.4 - + + -
487B LEU* 4.0 20.4 - - + -
488B PRO* 3.0 19.7 + - + +
490B GLU* 1.3 79.7 - - - +
492B LEU* 1.3 78.8 + - + +
494B LYS* 3.2 12.0 + - + +
495B VAL* 3.1 40.4 + - + +
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Residues in contact with LEU 492 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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484A TRP* 4.0 11.0 - - + -
513A MET* 3.7 31.9 - - + +
430B PHE* 5.2 6.7 - - + -
471B LEU* 5.7 0.9 - - + -
487B LEU* 3.0 49.8 - - + +
488B PRO 3.0 20.1 + - - +
489B HIS* 4.0 5.6 - - - +
491B PHE* 1.3 92.0 - - + +
493B SER* 1.3 67.4 + - - +
495B VAL* 3.1 7.8 + - + +
496B SER* 2.9 26.2 + - - -
511B TYR* 4.7 20.4 - - + -
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Residues in contact with SER 493 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484A TRP* 2.9 27.7 + - - +
515A ASN* 5.2 8.6 + - - -
489B HIS* 2.9 29.9 + - - -
490B GLU* 3.7 6.3 - - - -
492B LEU* 1.3 76.9 - - - +
494B LYS* 1.3 61.9 + - - +
496B SER* 3.0 8.0 + - - -
497B HIS* 2.9 27.9 + - - +
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Residues in contact with LYS 494 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433B GLU* 3.1 35.2 + - + -
436B LYS* 5.0 9.8 - - - +
437B SER* 5.6 3.5 + - - -
490B GLU 3.2 12.0 + - - +
491B PHE* 3.5 15.0 - - + +
492B LEU 3.2 0.6 - - - -
493B SER* 1.3 78.5 - - - +
495B VAL* 1.3 66.3 + - + +
497B HIS* 3.7 4.9 - - - +
498B ARG* 3.1 29.6 + - - +
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Residues in contact with VAL 495 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429B ILE* 4.9 2.5 - - + -
430B PHE* 3.9 20.9 - - + -
433B GLU* 3.9 33.7 - - + -
471B LEU* 3.8 28.3 - - + -
491B PHE* 3.1 31.0 + - + +
492B LEU* 3.1 9.2 + - + +
494B LYS* 1.3 74.4 - - - +
496B SER* 1.3 58.1 + - - +
498B ARG* 2.9 10.9 + - - +
499B ILE* 2.9 38.0 + - + +
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Residues in contact with SER 496 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513A MET* 2.9 40.9 + - - -
514A THR* 4.9 2.6 - - - -
492B LEU 2.9 16.7 + - - -
493B SER* 3.0 12.3 + - - -
495B VAL* 1.3 73.2 - - - +
497B HIS* 1.3 71.9 + - - +
499B ILE* 3.2 2.8 + - - +
500B VAL* 3.1 30.2 + - - +
509B VAL* 3.6 24.7 - - - +
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Residues in contact with HIS 497 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A THR* 6.4 0.9 - - - -
515A ASN* 5.1 11.4 - - - -
517A PRO* 5.7 3.4 - - - +
518A PRO* 4.4 28.5 - - + +
493B SER 2.9 15.6 + - - +
494B LYS* 3.7 6.5 - - - +
496B SER* 1.3 80.8 + - - +
498B ARG* 1.3 56.3 + - - +
500B VAL* 3.6 2.8 + - - +
501B ASN* 2.7 59.6 + - - -
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Residues in contact with ARG 498 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429B ILE* 3.7 32.0 + - + +
432B GLU* 2.7 38.9 + - - +
433B GLU* 3.2 24.3 + - - +
436B LYS* 5.0 3.1 - - - +
494B LYS* 3.1 20.2 + - - +
495B VAL* 2.9 11.7 + - - +
497B HIS* 1.3 75.6 - - - +
499B ILE* 1.3 64.7 + - - +
501B ASN* 4.8 2.0 - - - +
502B GLU* 2.8 89.8 + - + +
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Residues in contact with ILE 499 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426B ALA* 3.9 25.4 - - + +
429B ILE* 4.1 22.0 - - + -
430B PHE* 5.0 0.4 - - + -
469B ILE* 4.5 21.8 - - + -
471B LEU* 4.1 22.0 - - + -
495B VAL* 2.9 35.1 + - + +
496B SER* 3.2 6.3 + - - +
498B ARG* 1.3 77.2 - - - +
500B VAL* 1.3 59.6 + - - +
503B ILE* 3.3 41.8 + - + +
506B VAL* 4.4 7.8 - - + +
509B VAL* 4.7 9.9 - - + -
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Residues in contact with VAL 500 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A THR* 4.4 6.5 - - + -
518A PRO* 4.4 24.5 - - + +
496B SER 3.1 8.9 + - - +
497B HIS* 4.3 3.1 - - - +
499B ILE* 1.3 75.2 - - - +
501B ASN* 1.3 65.4 + - - +
503B ILE 3.0 17.6 - - - +
504B LYS* 4.7 1.9 - - - -
506B VAL* 3.9 9.6 + - + -
507B SER* 3.6 23.2 + - - +
508B ARG* 3.2 24.5 - - - +
509B VAL* 3.4 26.9 - - + -
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Residues in contact with ASN 501 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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518A PRO* 4.9 10.6 - - - +
497B HIS* 2.7 62.5 + - - +
498B ARG* 4.3 3.1 - - - +
500B VAL* 1.3 80.9 - - - +
502B GLU* 1.3 66.0 + - + +
503B ILE 4.3 2.4 - - - -
504B LYS* 4.5 2.6 + - - +
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Residues in contact with GLU 502 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425B GLN* 4.7 6.2 + - - +
429B ILE* 3.5 18.5 - - + +
498B ARG* 2.8 65.1 + - + +
501B ASN* 1.3 79.1 - - + +
503B ILE* 1.3 62.4 + - + +
504B LYS* 3.5 3.5 + - - +
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Residues in contact with ILE 503 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422B ILE* 3.9 14.8 - - + +
425B GLN* 3.4 33.9 - - + +
426B ALA* 3.3 40.2 - - + +
429B ILE* 4.5 9.6 - - + -
499B ILE* 3.3 25.9 + - + +
500B VAL 3.0 18.4 - - - +
501B ASN 4.3 0.2 - - - -
502B GLU* 1.3 75.1 - - + +
504B LYS* 1.3 75.8 + - - +
505B GLU* 3.7 12.3 - - - +
506B VAL* 3.6 21.0 - - + +
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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