Contacts of the helix formed by residues 633 - 649 (chain D) in PDB entry 2BKU
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 PHE 633 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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599D MET* 4.0 13.0 - - + -
622D ILE* 3.4 33.9 - - + -
625D LEU* 5.0 0.9 - - + -
626D ALA* 3.6 31.0 - - + +
629D LEU* 3.6 16.8 - - + +
630D GLY 3.1 14.1 + - - +
632D GLY* 1.3 74.7 - - - +
634D GLU* 1.3 65.9 + - - +
635D LYS 3.2 2.9 - - - -
636D TYR* 2.9 42.0 + + + -
637D LEU* 3.3 13.6 + - + -
640D PHE* 3.7 16.6 - + + -
662D PHE* 3.6 28.3 - + - -
666D ILE* 4.4 9.2 - - + -
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Residues in contact with GLU 634 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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630D GLY 4.5 0.8 + - - -
631D LYS* 3.3 17.2 + - - +
633D PHE* 1.3 76.9 - - - +
635D LYS* 1.3 62.4 + - - +
637D LEU* 3.0 24.6 + - + +
638D GLU* 4.2 2.9 + - - +
666D ILE* 5.8 1.0 - - - +
670D LEU* 3.7 28.1 - - + +
673D ASP* 4.7 12.5 - - - +
676D ARG* 3.7 16.7 + - - -
677D TYR* 2.6 39.4 + - + +
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Residues in contact with LYS 635 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595D ALA* 5.5 4.0 - - - +
629D LEU* 5.6 1.0 - - - +
632D GLY* 3.7 16.0 + - - +
633D PHE 3.1 0.2 + - - -
634D GLU* 1.3 76.3 - - - +
636D TYR* 1.3 103.5 + - + +
638D GLU* 5.1 6.9 + - - +
639D THR* 5.1 4.7 - - - +
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Residues in contact with TYR 636 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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595D ALA* 3.5 7.4 - - - +
596D ASP* 3.5 32.6 + - + +
599D MET* 3.7 32.3 - - + -
603D PHE* 4.1 19.7 - + + -
629D LEU* 3.8 20.0 - - + -
632D GLY 4.0 0.9 - - - -
633D PHE* 2.9 39.4 + + + +
635D LYS* 1.3 115.1 + - + +
637D LEU* 1.3 66.0 + - - +
638D GLU 3.0 3.8 + - - -
639D THR* 3.1 8.1 + - - +
640D PHE* 2.9 23.2 + - - +
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Residues in contact with LEU 637 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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633D PHE* 3.3 10.9 + - + +
634D GLU* 3.0 19.8 + - + +
636D TYR* 1.3 75.4 - - - +
638D GLU* 1.3 63.5 + - - +
640D PHE* 3.7 7.0 - - + -
641D SER* 2.9 29.3 + - - +
644D LEU* 5.4 5.8 - - + -
662D PHE* 4.8 21.8 - - + -
666D ILE* 4.8 15.9 - - + -
670D LEU* 4.0 16.6 - - + -
674D PHE* 6.0 0.2 - - + -
677D TYR* 3.8 51.8 - - + +
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Residues in contact with GLU 638 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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634D GLU 4.2 3.1 + - - +
635D LYS 5.1 5.2 - - - +
636D TYR 4.6 1.1 - - - +
637D LEU* 1.3 82.6 - - - +
639D THR* 1.3 70.3 + - + +
641D SER* 3.2 21.6 - - - -
642D PRO* 3.9 3.3 - - - +
677D TYR* 5.4 6.9 - - + -
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Residues in contact with THR 639 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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603D PHE* 3.1 33.5 - - + -
635D LYS 5.1 6.1 - - - +
636D TYR* 3.1 6.8 + - - +
638D GLU* 1.3 87.3 - - + +
640D PHE* 1.3 56.9 + - - +
642D PRO* 3.4 14.8 - - - +
643D TYR* 3.6 15.9 - - - -
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Residues in contact with PHE 640 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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603D PHE* 3.8 12.6 - + + -
606D LEU* 5.6 0.2 - - + -
619D PHE* 3.4 37.2 - + - -
622D ILE* 3.5 43.3 - - + -
623D SER* 4.9 1.8 - - - -
633D PHE* 3.7 18.8 - + + -
636D TYR 2.9 18.9 + - - +
637D LEU* 3.8 5.6 - - + +
639D THR* 1.3 76.7 + - - +
641D SER* 1.3 64.9 + - - +
642D PRO* 3.3 1.8 - - - -
643D TYR* 3.0 30.4 + + + +
644D LEU* 3.1 19.3 + - + -
662D PHE* 3.5 39.7 - + - -
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Residues in contact with SER 641 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637D LEU* 2.9 19.8 + - - -
638D GLU* 3.2 18.6 - - - -
640D PHE* 1.3 75.2 - - - +
642D PRO* 1.4 66.2 - - - +
644D LEU* 3.1 18.3 + - - +
645D LEU* 3.1 28.3 + - - +
681D MET* 5.6 4.0 - - - +
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Residues in contact with PRO 642 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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638D GLU 3.9 2.5 - - - +
639D THR* 3.4 16.4 - - - +
640D PHE 3.3 5.6 - - - -
641D SER* 1.4 95.1 - - - +
643D TYR* 1.3 63.8 + - + +
645D LEU* 3.4 10.1 + - + +
646D LYS* 2.9 29.9 + - - +
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Residues in contact with TYR 643 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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603D PHE* 3.9 21.5 + + - -
606D LEU* 3.4 62.7 + - + +
607D GLU* 3.8 11.4 + - - +
615D GLU* 6.3 0.7 - - + -
619D PHE* 3.9 7.8 - - + -
639D THR 3.6 24.2 - - - -
640D PHE* 3.0 25.0 + + + +
642D PRO* 1.3 80.8 - - + +
644D LEU* 1.3 61.0 + - - +
646D LYS* 3.7 11.3 - - + +
647D ALA* 3.0 28.9 + - - +
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Residues in contact with LEU 644 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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619D PHE* 3.9 25.3 - - + -
637D LEU* 5.4 8.7 - - + -
640D PHE* 3.1 16.5 + - + +
641D SER* 3.1 12.3 + - - +
643D TYR* 1.3 74.6 - - - +
645D LEU* 1.3 53.5 + - + +
647D ALA* 3.1 3.3 + - - +
648D LEU* 2.7 46.9 + - + +
659D ALA* 4.0 14.6 - - + +
662D PHE* 3.3 41.7 - - + -
663D ILE* 4.3 2.5 - - + -
666D ILE* 6.1 0.4 - - + -
681D MET* 3.7 33.4 - - + -
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Residues in contact with LEU 645 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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641D SER* 3.1 26.5 + - - +
642D PRO* 3.8 9.4 - - + +
644D LEU* 1.3 77.4 - - + +
646D LYS* 1.3 65.5 + - - +
648D LEU* 3.3 10.2 + - + +
649D ASN* 2.9 37.3 + - - +
680D ALA* 4.9 4.3 - - + +
681D MET* 3.9 23.8 - - + -
684D VAL* 3.7 31.4 - - + -
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Residues in contact with LYS 646 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C LYS* 3.4 29.2 - - - +
615D GLU* 3.5 15.0 + - - +
642D PRO 2.9 18.8 + - - +
643D TYR* 3.7 14.1 - - + +
645D LEU* 1.3 77.7 - - - +
647D ALA* 1.3 60.0 + - - +
649D ASN* 3.8 5.8 + - - +
650D GLN* 3.0 34.2 + - + +
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Residues in contact with ALA 647 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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619D PHE* 3.7 29.6 - - + -
643D TYR 3.0 19.2 + - - +
644D LEU 3.1 3.6 + - - +
646D LYS* 1.3 75.0 - - - +
648D LEU* 1.3 65.6 + - - +
650D GLN* 3.0 26.8 + - - +
655D VAL* 3.9 16.6 - - + +
656D SER* 3.6 15.4 + - - -
659D ALA* 4.1 2.5 - - + -
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Residues in contact with LEU 648 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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644D LEU* 2.7 41.1 + - + +
645D LEU* 3.7 24.7 - - + +
647D ALA* 1.3 72.3 - - - +
649D ASN* 1.3 60.4 + - - +
650D GLN 3.4 0.5 + - - -
651D VAL* 3.8 2.3 - - - +
656D SER* 3.6 13.6 - - - +
659D ALA* 3.9 23.3 - - + +
660D VAL* 4.2 3.6 - - + +
663D ILE* 3.5 31.6 - - + -
681D MET* 4.2 5.4 - - - -
684D VAL* 4.1 12.8 - - + -
685D LEU* 4.5 1.8 - - + -
688D MET* 3.3 47.4 - - + +
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Residues in contact with ASN 649 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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645D LEU* 2.9 30.2 + - - +
646D LYS* 4.2 6.4 - - - +
647D ALA 3.2 0.4 - - - -
648D LEU* 1.3 74.0 - - - +
650D GLN* 1.3 58.1 + - + +
651D VAL* 2.7 24.3 + - - +
684D VAL* 4.2 19.7 - - - +
687D GLN* 4.9 13.9 - - - +
688D MET* 4.9 4.4 - - - +
691D ASN* 5.4 0.7 - - - +
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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