Contacts of the strand formed by residues 663 - 675 (chain B) in PDB entry 3HI7
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 GLU 663 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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525B THR 3.9 1.6 - - - -
526B LYS* 4.0 18.6 + - - -
527B ASN 2.8 29.1 + - - +
626B LYS* 3.3 33.7 + - + -
659B ASN* 3.4 29.5 - - - +
660B ILE* 4.1 2.2 - - - -
661B GLU 3.4 11.8 - - - +
662B ASN* 1.3 85.2 - - - +
664B ASP* 1.3 63.2 + - - +
665B LEU* 3.2 23.3 + - + +
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Residues in contact with ASP 664 (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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79B LYS* 2.8 26.0 + - - +
519B ASP* 3.5 2.1 - - - +
521B ASP* 3.2 1.4 - - - +
525B THR* 3.1 32.8 + - + +
526B LYS* 4.5 4.7 - - + +
626B LYS* 3.6 8.9 - - + +
627B TYR* 2.8 49.4 + - + +
663B GLU* 1.3 72.0 + - - +
665B LEU* 1.3 59.6 + - - +
802B CA 2.3 32.4 - - - -
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Residues in contact with LEU 665 (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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519B ASP* 3.1 3.8 - - - +
520B LEU* 3.3 8.7 + - - +
525B THR 4.4 0.8 + - - -
527B ASN* 3.7 24.1 - - + +
528B SER* 3.7 24.5 - - - +
529B PHE* 4.0 12.3 - - + +
579B PHE* 4.5 11.0 - - + -
624B VAL* 4.1 12.3 - - + -
625B THR 3.4 7.0 - - - +
626B LYS* 4.8 0.2 - - - -
660B ILE* 3.5 42.8 - - + +
663B GLU* 3.2 19.5 + - + +
664B ASP* 1.3 79.2 + - - +
666B VAL* 1.3 62.5 + - - +
667B ALA 4.4 0.2 + - - -
802B CA 2.4 27.9 - - - -
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Residues in contact with VAL 666 (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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517B ARG* 3.7 51.8 - - + +
518B VAL 4.0 6.1 - - - +
519B ASP* 3.7 14.1 - - - +
624B VAL* 3.3 6.0 - - - -
625B THR* 2.8 44.4 + - - +
627B TYR* 3.8 24.7 - - + -
665B LEU* 1.3 80.5 - - - +
667B ALA* 1.3 70.4 - - - +
668B TRP* 3.6 12.2 - - - +
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Residues in contact with ALA 667 (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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518B VAL* 2.7 54.5 + - + +
520B LEU* 5.1 2.7 - - + -
579B PHE* 3.6 33.0 - - + -
595B LEU* 4.8 5.2 - - + -
622B LEU* 3.9 11.7 - - + -
623B ALA 3.5 4.7 - - - -
624B VAL* 4.5 1.8 - - - +
665B LEU 4.2 0.6 - - - -
666B VAL* 1.3 76.2 - - - +
668B TRP* 1.3 58.9 + - - +
669B VAL* 4.8 0.7 - - + -
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Residues in contact with TRP 668 (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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353B GLN* 4.2 2.7 - - + -
515B HIS* 3.4 31.8 + + + +
516B TYR 3.4 4.9 - - - -
517B ARG* 3.1 55.4 - - + -
620B TYR 4.7 1.0 - - - +
621B PRO 4.2 0.5 - - - -
622B LEU* 3.4 5.9 - - - +
623B ALA* 2.8 40.1 + - + +
625B THR* 2.9 30.7 + - + +
631B GLU* 3.5 15.0 - - + -
632B LEU 4.0 5.8 - - - -
634B SER* 3.7 26.0 - - - -
650B PHE* 3.5 25.1 - + + -
653B PHE* 3.8 17.7 - + - -
666B VAL* 3.6 15.4 - - + +
667B ALA* 1.3 75.8 - - - +
669B VAL* 1.3 62.1 + - - +
670B THR 4.3 0.2 + - - -
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Residues in contact with VAL 669 (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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514B VAL 3.6 1.4 - - - +
515B HIS* 3.3 8.5 + - - -
516B TYR* 2.9 38.4 + - + +
518B VAL* 4.0 17.7 - - + -
595B LEU* 3.7 31.2 - - + -
597B ILE* 4.0 17.3 - - + -
621B PRO 3.2 9.2 - - - +
622B LEU* 4.3 3.8 - - + -
667B ALA* 4.8 1.1 - - + -
668B TRP* 1.3 79.7 - - - +
670B THR* 1.3 60.9 + - - +
671B VAL* 3.8 24.0 + - + -
694B PHE* 4.0 16.4 - - + -
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Residues in contact with THR 670 (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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513B LEU* 4.2 14.4 - - + -
514B VAL 3.3 9.0 - - - +
515B HIS* 3.3 11.5 - - - -
569B PHE* 4.2 18.5 - - + -
597B ILE* 4.4 3.5 - - - +
599B SER* 4.1 4.5 + - - -
601B ALA* 5.2 0.2 - - - -
617B TRP* 3.1 30.8 + - + -
618B ALA* 4.3 6.1 - - - -
620B TYR 2.9 24.6 + - - -
621B PRO* 3.0 24.2 + - - +
669B VAL* 1.3 72.8 - - - +
671B VAL* 1.3 74.5 + - - +
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Residues in contact with VAL 671 (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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479B MET* 6.1 0.2 - - + -
513B LEU* 3.5 2.8 - - - -
514B VAL* 2.8 48.7 + - + +
516B TYR* 4.1 15.7 - - + -
597B ILE* 3.8 9.9 - - + -
599B SER* 3.3 11.2 - - - -
601B ALA* 4.1 4.0 - - - -
669B VAL* 3.8 19.1 - - + -
670B THR* 1.3 80.8 - - - +
672B GLY* 1.3 58.2 + - - +
692B VAL* 3.7 25.1 - - + -
693B GLY* 3.5 28.7 - - - +
694B PHE* 4.9 1.6 - - + -
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Residues in contact with GLY 672 (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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512B HIS* 3.0 14.4 - - - -
513B LEU* 4.3 0.2 - - - -
514B VAL* 5.6 0.7 - - - -
599B SER* 3.0 7.3 + - - -
600B MET 2.8 25.3 + - - -
601B ALA* 3.2 10.8 + - - +
671B VAL* 1.3 78.3 - - - +
673B PHE* 1.3 70.2 + - - +
692B VAL* 3.5 13.2 - - - +
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Residues in contact with PHE 673 (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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479B MET* 4.4 18.6 - - + -
481B ALA* 4.2 17.7 - - + -
511B THR* 3.6 6.9 - - - +
512B HIS* 2.9 65.4 + + + -
600B MET* 4.0 35.2 - - + -
601B ALA* 4.5 1.0 - - - +
672B GLY* 1.3 79.9 - - - +
674B LEU* 1.3 73.4 + - - +
675B HIS* 3.7 13.3 + + + -
685B THR* 6.3 0.4 - - + -
689B GLY 6.2 0.2 - - - -
690B ASN* 3.9 34.5 - - + -
691B SER 5.4 0.2 - - - -
692B VAL* 4.0 15.5 - - + -
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Residues in contact with LEU 674 (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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533A GLN* 4.6 3.4 - - - -
534A MET* 4.0 37.9 - - + +
575A LYS* 4.4 21.5 - - + +
576A TYR* 3.2 38.9 + - + -
594A ARG* 4.8 4.7 + - - -
509B ILE* 4.0 15.7 - - + -
510B HIS 3.5 18.2 - - - +
511B THR* 3.6 19.3 - - + +
600B MET* 4.4 8.3 + - - +
673B PHE* 1.3 80.7 - - - +
675B HIS* 1.3 58.8 + - - +
676B ILE* 4.0 15.0 - - + -
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Residues in contact with HIS 675 (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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576A TYR* 3.4 4.5 - - - -
461B TPQ 3.5 5.6 - - - -
485B VAL* 3.8 7.9 - - + -
509B ILE* 3.9 0.2 - - - -
510B HIS* 2.8 43.6 + + - +
512B HIS* 3.8 9.8 + - + -
673B PHE* 3.7 11.9 + + + -
674B LEU* 1.3 72.0 - - - +
676B ILE* 1.3 75.0 + - - +
677B PRO* 3.3 9.8 - - + +
678B HIS* 4.8 5.0 + + - -
681B ASP* 2.8 26.6 + - - -
685B THR* 3.5 30.0 - - + +
690B ASN* 5.7 4.4 + - - -
801B CU 2.0 35.0 - - - -
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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