Contacts of the helix formed by residues 643 - 656 (chain D) in PDB entry 3T6A
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 ASP 643 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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556D VAL* 4.1 0.5 - - - +
557D LEU* 3.5 29.8 + - + -
560D ASP* 2.4 29.3 - - - +
637D LEU* 2.8 24.2 + - + +
641D MET* 4.2 2.9 - - + -
642D GLY* 1.3 75.1 - - - +
644D LEU* 1.3 58.0 + - - +
645D TYR* 3.3 5.0 + - - +
646D SER* 3.1 22.1 + - - -
647D PHE* 3.1 23.6 + - - +
707D VAL* 3.4 21.8 - - - +
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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
----------------------------------------------------------
638D LYS* 4.9 6.7 - - - -
642D GLY 4.5 4.9 - - - +
643D ASP* 1.3 72.1 - - - +
645D TYR* 1.3 65.3 + - - +
647D PHE* 3.5 7.3 - - + +
648D SER* 2.9 24.8 + - - -
687D PHE* 3.9 31.2 - - + -
691D LEU* 4.1 13.9 - - + -
696D GLU* 3.8 36.8 - - + +
701D PRO* 4.1 15.9 - - + -
705D VAL* 4.0 27.8 - - + -
707D VAL 2.9 14.1 + - - +
709D LEU* 3.8 15.5 - - - +
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Residues in contact with TYR 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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560D ASP* 3.6 33.4 - - + -
563D VAL* 6.1 0.9 - - + -
598D ILE* 2.6 47.8 + - + -
601D ARG* 3.3 21.6 - - + +
602D HIS* 3.2 43.6 + + + -
605D MET* 5.0 2.0 - - + -
643D ASP* 3.3 6.2 + - - +
644D LEU* 1.3 77.9 - - - +
646D SER* 1.3 70.1 + - - +
648D SER* 2.7 21.7 + - - -
649D ALA 3.2 4.9 + - - -
707D VAL* 3.7 9.6 - - + -
708D PRO 3.3 19.0 + - - +
709D LEU 3.6 20.2 - - - -
710D LEU* 4.2 10.1 - - + -
711D MET* 4.3 2.7 - - - -
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Residues in contact with SER 646 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556D VAL* 3.2 19.0 - - - +
560D ASP* 2.7 26.1 + - - -
605D MET* 3.1 30.1 - - - +
637D LEU* 3.9 7.9 - - - -
643D ASP* 3.1 9.3 + - - -
645D TYR* 1.3 77.5 - - - +
647D PHE* 1.3 65.3 + - - +
649D ALA* 3.3 6.9 + - - +
650D LEU* 3.2 28.4 + - - +
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Residues in contact with PHE 647 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634D ALA* 3.4 26.9 - - + -
637D LEU* 3.9 13.9 - - + +
638D LYS* 3.9 16.2 - - + +
643D ASP 3.1 20.7 + - - +
644D LEU* 3.5 7.0 - - - +
646D SER* 1.3 78.1 - - - +
648D SER* 1.3 65.8 + - - +
650D LEU* 3.4 3.7 + - - +
651D MET* 3.2 52.2 + - + +
684D LEU* 3.7 35.2 - - + -
687D PHE* 3.6 29.2 - + - -
688D SER* 4.3 10.5 - - - -
691D LEU* 4.0 20.9 - - + -
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Residues in contact with SER 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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602D HIS* 3.0 16.0 + - - -
644D LEU 2.9 7.2 + - - -
645D TYR* 2.7 19.3 + - - -
647D PHE* 1.3 82.2 - - - +
649D ALA* 1.3 56.1 + - - +
651D MET* 3.4 7.3 + - - +
652D LYS* 2.8 30.1 + - - +
688D SER* 5.4 4.7 - - - -
691D LEU* 5.7 0.9 - - - -
709D LEU* 3.4 32.6 + - - +
711D MET* 4.7 2.2 - - - +
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Residues in contact with ALA 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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602D HIS* 3.6 37.7 - - + +
605D MET* 3.9 27.8 - - + -
606D ALA* 3.7 12.4 - - - +
609D ILE* 5.3 0.2 - - - -
645D TYR 3.2 3.6 + - - +
646D SER* 3.3 10.5 + - - +
648D SER* 1.3 81.5 + - - +
650D LEU* 1.3 62.4 + - - +
652D LYS* 3.3 5.0 + - - +
653D ALA* 3.2 17.7 + - - +
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Residues in contact with LEU 650 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556D VAL* 6.1 1.6 - - + -
605D MET* 4.3 13.7 - - - -
609D ILE* 3.7 30.5 - - + -
630D ILE* 3.7 33.9 - - + +
633D VAL* 3.9 17.0 - - + -
634D ALA* 3.8 24.5 - - + +
637D LEU* 4.0 10.5 - - + -
646D SER* 3.2 15.7 + - - +
647D PHE 3.9 6.7 - - - +
649D ALA* 1.3 76.0 - - - +
651D MET* 1.3 62.2 + - - +
653D ALA* 3.0 16.9 + - - +
654D LEU* 3.2 19.9 + - + +
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Residues in contact with MET 651 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634D ALA* 4.9 4.3 - - + -
647D PHE* 3.2 46.4 + - + +
648D SER* 3.6 7.9 - - - +
650D LEU* 1.3 76.0 - - - +
652D LYS* 1.3 62.9 + - - +
654D LEU* 3.5 9.8 + - - +
655D GLU* 3.1 37.3 + - - +
680D TYR* 3.6 35.4 + - + +
684D LEU* 4.0 34.5 - - + +
685D LYS* 4.1 8.7 - - + +
688D SER* 3.9 20.4 - - - +
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Residues in contact with LYS 652 (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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602D HIS* 4.3 15.7 + - + -
603D ASN* 3.8 12.9 + - - +
606D ALA* 3.7 20.1 - - + +
648D SER 2.8 20.4 + - - +
649D ALA* 3.4 8.1 - - - +
650D LEU 3.2 0.2 - - - -
651D MET* 1.3 74.4 - - - +
653D ALA* 1.3 57.7 + - - +
655D GLU* 3.3 9.8 + - + +
656D MET* 3.2 35.3 + - + +
724D PHE* 2.9 44.2 + - - +
725D GLU* 5.4 1.1 - - - -
727D THR* 2.9 36.6 + - + +
728D ASP* 5.5 1.3 - - - +
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Residues in contact with ALA 653 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606D ALA 3.7 22.0 - - - +
609D ILE* 3.7 25.1 - - + -
610D ALA* 4.3 7.2 - - - +
613D ILE* 5.7 1.3 - - + -
649D ALA 3.2 5.6 + - - +
650D LEU 3.0 9.5 + - - +
652D LYS* 1.3 75.8 - - - +
654D LEU* 1.3 62.6 + - + +
655D GLU 3.0 5.8 + - - -
656D MET* 3.2 20.7 + - + +
659D ILE* 3.4 21.2 - - - +
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Residues in contact with LEU 654 (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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613D ILE* 4.3 9.4 - - + -
627D LEU* 3.4 33.0 - - + -
630D ILE* 3.9 22.7 - - + -
631D ILE* 4.0 17.9 - - + -
634D ALA* 5.7 1.3 - - + -
650D LEU* 3.2 16.3 + - + +
651D MET* 4.0 12.6 - - - +
652D LYS 3.5 0.2 - - - -
653D ALA* 1.3 75.7 - - + +
655D GLU* 1.3 59.0 + - - +
656D MET 3.5 0.2 - - - -
659D ILE* 4.0 6.9 - - - +
660D THR* 3.5 14.2 - - - +
666D TRP* 3.7 17.2 - - + -
680D TYR* 3.5 43.9 + - + +
684D LEU* 6.2 0.2 - - + -
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Residues in contact with GLU 655 (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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651D MET* 3.1 32.6 + - + +
652D LYS* 3.7 7.8 - - - +
653D ALA 3.0 0.8 - - - -
654D LEU* 1.3 77.0 - - - +
656D MET* 1.3 70.2 + - - +
657D PRO* 3.5 2.9 - - - +
660D THR* 3.5 12.6 - - - +
680D TYR* 4.2 11.4 - - - +
685D LYS* 5.3 10.6 - - - +
688D SER* 4.2 15.2 + - - -
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Residues in contact with MET 656 (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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606D ALA* 3.4 41.1 - - + +
607D ILE* 4.2 0.9 - - - +
610D ALA* 3.8 21.5 - - + -
652D LYS* 3.2 20.9 + - + +
653D ALA* 3.2 15.1 + - - +
655D GLU* 1.3 79.3 - - - +
657D PRO* 1.3 68.9 - - + +
658D GLN* 4.0 6.1 - - - +
659D ILE* 2.9 9.7 + - + -
660D THR* 2.9 26.2 + - - +
724D PHE* 3.5 39.9 - - + -
725D GLU* 4.0 9.4 - - - +
808D LEU* 4.3 4.9 - - - -
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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
------------------------------------------------------------
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