Contacts of the helix formed by residues 644 - 661 (chain D) in PDB entry 4YFI
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 ILE 644 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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578D HIS* 3.3 62.5 - - + +
583D PRO* 5.0 4.0 - - + -
584D ILE 4.7 1.6 - - - +
585D ILE* 4.0 20.8 - - + +
613D LEU* 4.4 24.7 - - + +
643D THR* 1.3 74.7 - - - +
645D LYS* 1.3 74.7 + - + +
647D ASP* 3.1 12.6 + - - +
648D VAL* 3.6 4.4 + - + +
711D GLU* 4.2 20.4 - - - +
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Residues in contact with LYS 645 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643D THR* 3.1 13.3 - - - +
644D ILE* 1.3 87.0 - - + +
646D ALA* 1.3 61.0 + - - +
648D VAL* 3.3 17.5 + - + +
649D PHE 3.4 6.2 + - - -
706D PRO* 3.4 35.3 + - + +
707D GLU* 3.8 14.3 + - + +
709D ARG* 2.8 46.4 + - + +
710D PRO 4.1 13.0 - - - +
711D GLU* 4.1 30.5 + - - +
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Residues in contact with ALA 646 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632C ALA* 3.8 8.6 - - + +
634C GLU* 3.6 20.2 - - - +
635C VAL* 3.6 11.4 - - + -
642D TYR* 3.3 38.4 - - + +
643D THR* 3.2 6.3 + - - +
644D ILE 3.1 1.0 - - - -
645D LYS* 1.3 76.9 - - - +
647D ASP* 1.3 63.6 + - - +
649D PHE* 3.5 4.0 + - - +
650D SER* 2.9 27.5 + - - -
709D ARG* 3.9 0.4 - - - +
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Residues in contact with ASP 647 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574D MET* 3.2 23.7 - - + +
578D HIS* 3.1 20.5 + - + +
585D ILE* 3.3 12.9 - - - +
586D HIS* 2.8 24.7 + - - +
587D ARG* 3.0 26.9 + - - -
588D ASP 4.5 1.2 + - - -
589D LEU* 4.0 7.9 - - - +
642D TYR* 4.1 1.2 + - - -
644D ILE 3.1 11.6 + - - +
646D ALA* 1.3 79.4 - - - +
648D VAL* 1.3 56.8 + - - +
650D SER* 3.4 7.1 + - - -
651D TYR* 2.9 28.9 + - - +
712D PHE* 4.0 1.7 - - - -
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Residues in contact with VAL 648 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578D HIS* 4.7 1.3 - - + +
644D ILE* 3.8 12.3 - - + +
645D LYS* 3.3 17.9 + - + +
646D ALA 3.2 0.2 - - - -
647D ASP* 1.3 75.6 - - - +
649D PHE* 1.3 55.6 + - - +
651D TYR* 3.3 4.6 + - + +
652D ALA* 2.8 32.1 + - - +
701D GLY* 3.9 8.0 - - - +
709D ARG* 3.8 17.3 - - + -
710D PRO* 3.4 38.6 - - + +
711D GLU* 5.1 0.9 - - - -
712D PHE* 3.6 33.7 - - + +
715D VAL* 5.3 5.4 - - + -
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Residues in contact with PHE 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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631C MET 3.3 19.5 - - - -
632C ALA* 3.6 16.2 - - + -
633C PRO* 3.4 22.4 - - + -
645D LYS 3.4 2.4 + - - -
646D ALA 3.7 9.0 - - - +
647D ASP 3.3 0.2 - - - -
648D VAL* 1.3 77.0 - - - +
650D SER* 1.3 67.3 + - - +
652D ALA* 3.1 12.0 + - - +
653D LEU* 3.2 31.7 + - + +
677D MET* 3.8 17.5 - - - -
683D ARG* 3.7 12.1 - - - -
701D GLY 3.4 10.3 + - - +
702D TRP* 3.2 43.3 - - + -
709D ARG* 3.6 33.2 - - - +
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Residues in contact with SER 650 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
630C TRP* 3.0 28.4 + - - -
631C MET* 4.4 1.6 - - - -
632C ALA 4.2 5.0 + - - -
587D ARG 5.8 1.4 - - - -
588D ASP 5.7 1.2 + - - -
589D LEU* 3.5 30.1 + - - -
642D TYR* 5.4 1.7 + - - -
646D ALA 2.9 15.2 + - - -
647D ASP* 3.7 9.4 + - - -
649D PHE* 1.3 78.1 - - - +
651D TYR* 1.3 62.5 + - - +
653D LEU* 3.4 6.7 + - - +
654D CYS* 3.2 24.2 + - - -
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Residues in contact with TYR 651 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567D ALA* 2.7 32.6 + - + +
570D VAL* 3.6 33.7 - - + -
571D ALA* 3.8 10.9 - - + +
589D LEU* 3.7 11.6 - - + +
647D ASP 2.9 19.4 + - - +
648D VAL* 3.4 7.2 - - + +
649D PHE 3.1 0.2 - - - -
650D SER* 1.3 73.9 - - - +
652D ALA* 1.3 59.1 + - - +
654D CYS* 2.9 11.5 + - + +
655D LEU* 2.8 53.7 + - + +
658D ILE* 5.8 1.8 - - + -
712D PHE* 3.5 24.5 - + + -
715D VAL* 3.7 22.4 - - + -
719D LEU* 3.1 18.4 - - - +
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Residues in contact with ALA 652 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648D VAL 2.8 16.3 + - - +
649D PHE 3.3 10.1 - - - +
651D TYR* 1.3 77.7 - - - +
653D LEU* 1.3 62.2 + - - +
655D LEU* 3.1 3.9 + - - +
656D TRP* 3.1 20.1 + - - +
698D LEU* 3.3 19.8 - - + +
701D GLY* 3.7 28.9 - - - -
702D TRP* 3.8 18.6 - - + +
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Residues in contact with LEU 653 (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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629C ARG 3.6 23.3 - - - +
630C TRP* 3.8 25.4 - - + +
649D PHE* 3.2 33.4 + - + +
650D SER 3.7 5.8 - - - +
651D TYR 3.2 0.2 - - - -
652D ALA* 1.3 75.5 - - - +
654D CYS* 1.3 53.1 + - - +
656D TRP* 3.4 4.7 + - - +
657D GLU* 2.8 36.5 + - - +
664D PRO* 4.1 17.2 - - + +
677D MET* 3.8 14.6 - - + -
684D PRO* 3.7 35.2 - - + -
702D TRP* 4.0 10.5 - - + -
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Residues in contact with CYS 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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630C TRP* 3.9 5.8 - - - -
547D LEU* 5.1 1.3 - - + +
570D VAL* 5.9 0.2 - - + -
589D LEU* 4.0 9.4 - - - -
590D ASN* 3.5 39.3 - - - -
591D SER 3.9 2.2 - - - -
594D ILE* 4.0 19.3 - - + -
650D SER 3.2 17.9 + - - -
651D TYR* 2.9 16.2 + - + +
653D LEU* 1.3 75.7 - - - +
655D LEU* 1.3 57.0 + - - +
657D GLU* 3.3 11.9 + - - +
658D ILE* 2.8 39.4 + - + +
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Residues in contact with LEU 655 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564D LEU* 5.2 2.9 - - + -
567D ALA* 3.6 29.6 - - + -
651D TYR* 2.8 40.2 + - + +
652D ALA* 3.1 9.8 + - - +
654D CYS* 1.3 69.2 - - - +
656D TRP* 1.3 66.0 + - - +
658D ILE* 3.3 10.6 + - + +
659D LEU* 3.1 47.6 + - + +
694D ILE* 4.1 16.2 - - + -
697D LEU* 4.9 11.4 - - + -
698D LEU* 3.9 17.5 - - + -
719D LEU* 4.5 16.2 - - + -
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Residues in contact with TRP 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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652D ALA 3.1 12.5 + - - +
653D LEU* 3.7 5.4 - - - +
655D LEU* 1.3 75.3 - - - +
657D GLU* 1.3 78.4 + - - +
659D LEU* 3.2 4.9 + - - +
660D THR* 2.9 61.2 + - + +
662D GLU* 3.3 33.9 - - + -
663D ILE 3.8 2.5 - - - -
664D PRO* 3.5 31.4 - - + -
665D PHE 4.9 2.5 - - - -
684D PRO* 3.3 25.5 - - + +
685D PRO* 2.9 37.2 + - + -
686D ILE* 4.8 0.4 - - + -
690D ILE* 4.1 13.4 - - + +
698D LEU* 3.7 12.6 - - + +
702D TRP* 3.8 27.8 - + + -
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Residues in contact with GLU 657 (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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630C TRP* 2.7 39.6 + - - -
547D LEU* 5.6 0.2 - - - -
551D LEU* 3.4 13.3 - - + +
552D HIS* 2.7 24.2 + - - +
591D SER* 2.5 35.1 + - - -
653D LEU 2.8 15.7 + - - +
654D CYS* 3.4 10.8 - - - +
656D TRP* 1.3 79.7 - - - +
658D ILE* 1.3 57.1 + - + +
660D THR* 4.0 0.4 - - - -
661D GLY* 3.1 22.0 + - - -
662D GLU 3.5 21.6 + - - +
663D ILE* 4.8 0.3 - - - -
664D PRO* 4.1 10.2 - - + +
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Residues in contact with ILE 658 (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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547D LEU* 3.7 34.5 - - + -
551D LEU* 3.9 14.8 - - + +
558D LEU* 5.7 0.7 - - + -
563D LYS* 3.4 52.9 + - + +
566D ILE* 4.1 17.9 - - + -
567D ALA* 4.2 18.4 - - + -
570D VAL* 5.7 2.2 - - + -
594D ILE* 5.7 2.0 - - + -
651D TYR* 5.8 2.7 - - + -
654D CYS* 2.8 35.3 + - + +
655D LEU* 3.5 11.4 - - + +
657D GLU* 1.3 75.6 - - - +
659D LEU* 1.3 65.2 + - + +
661D GLY* 3.8 4.2 + - - -
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Residues in contact with LEU 659 (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 LEU* 3.9 27.8 - - + -
563D LYS* 2.6 37.0 + - + +
564D LEU* 5.0 4.7 - - + -
655D LEU* 3.1 31.3 + - + +
656D TRP* 3.9 4.7 - - - +
658D ILE* 1.3 78.6 - - + +
660D THR* 1.3 59.0 + - - +
689D SER* 5.1 5.2 + - - -
690D ILE* 4.2 27.8 - - + -
691D PRO* 5.5 4.3 - - + -
694D ILE* 3.5 39.7 - - + -
698D LEU* 5.0 1.3 - - + -
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Residues in contact with THR 660 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563D LYS* 5.0 2.1 + - - -
656D TRP* 2.9 58.8 + - + +
659D LEU* 1.3 76.4 - - - +
661D GLY* 1.3 63.1 + - - +
662D GLU* 3.1 31.7 + - - +
685D PRO 5.0 1.3 - - - +
689D SER* 5.6 4.0 - - - +
690D ILE* 4.4 12.3 - - + -
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Residues in contact with GLY 661 (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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551D LEU* 3.7 24.8 - - - +
552D HIS* 3.5 16.7 + - - -
555D LYS* 5.5 2.3 - - - +
563D LYS* 5.8 1.3 - - - -
657D GLU 3.1 14.3 + - - -
658D ILE 3.8 5.0 + - - -
659D LEU 3.5 2.0 - - - -
660D THR* 1.3 79.1 + - - +
662D GLU* 1.3 62.7 + - - +
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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
------------------------------------------------------------
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