Contacts of the helix formed by residues 694 - 712 (chain D) in PDB entry 3F7F
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 ASN 694 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341D GLU* 4.4 2.7 + - - +
468D ASP* 5.4 3.8 - - + +
469D GLU* 3.0 25.6 - - + +
470D ILE* 3.4 11.8 - - - +
692D PHE* 4.5 0.5 - - - +
693D PHE* 1.3 78.1 + - + +
695D TYR* 1.3 62.9 + - - +
696D GLY* 3.9 4.3 - - - -
697D GLN* 2.6 65.6 + - - +
698D LEU* 3.3 15.6 + - - +
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Residues in contact with TYR 695 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D LEU* 4.4 2.1 - - + +
340D LEU* 3.8 28.5 - - + -
341D GLU* 4.1 1.8 - - + +
469D GLU* 2.7 47.1 + - + +
470D ILE* 3.7 18.8 - - + +
471D ILE* 2.8 29.4 + - + +
483D LEU* 5.0 0.4 - - + -
484D TYR 2.7 29.8 + - - -
485D LYS* 3.9 4.7 - - + -
486D LEU* 3.6 49.8 - - + -
694D ASN* 1.3 70.3 - - - +
696D GLY* 1.3 59.5 + - - +
698D LEU* 3.2 15.0 + - + +
699D ILE* 2.8 36.9 + - + +
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Residues in contact with GLY 696 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341D GLU* 3.8 17.0 + - - -
694D ASN* 3.3 5.5 + - - -
695D TYR* 1.3 79.6 - - - +
697D GLN* 1.3 55.7 + - - +
699D ILE* 3.8 6.6 - - - +
700D ALA* 2.8 32.9 + - - +
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Residues in contact with GLN 697 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600D ASP 4.6 16.4 - - - +
601D PHE* 4.5 5.1 - - - -
602D ILE* 4.3 7.8 + - - +
691D LYS 4.0 2.8 - - - +
692D PHE* 3.6 17.1 - - + +
693D PHE* 2.8 38.5 + - - +
694D ASN* 2.6 52.7 + - - +
696D GLY* 1.3 71.8 - - - -
698D LEU* 1.3 57.3 + - - +
700D ALA* 3.3 7.0 + - - +
701D TYR* 2.9 30.3 + - - +
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Residues in contact with LEU 698 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470D ILE* 5.1 2.0 - - + -
483D LEU* 4.4 15.9 - - + -
485D LYS* 3.7 33.4 - - + -
614D ILE* 4.4 9.9 - - + -
615D SER* 5.0 1.3 - - - +
618D SER* 5.0 0.4 - - - +
692D PHE* 3.5 50.2 - - + +
694D ASN 3.3 11.6 + - - +
695D TYR* 3.2 19.2 + - + +
696D GLY 3.2 0.6 - - - -
697D GLN* 1.3 75.9 - - - +
699D ILE* 1.3 66.9 + - - +
701D TYR* 3.2 5.6 + - + +
702D ILE* 3.0 43.4 + - + +
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Residues in contact with ILE 699 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341D GLU* 5.7 0.9 - - - +
485D LYS* 4.5 8.5 - - + +
486D LEU* 4.0 38.8 - - + +
487D ASN 5.0 0.7 - - - +
488D THR* 3.9 28.0 - - + +
695D TYR* 2.8 28.4 + - + +
696D GLY* 3.8 6.1 - - - +
698D LEU* 1.3 74.9 - - + +
700D ALA* 1.3 59.1 + - - +
702D ILE* 3.1 8.2 + - + +
703D ASP* 2.8 44.6 + - - +
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Residues in contact with ALA 700 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596D PHE* 4.9 3.0 - - + -
599D LYS* 5.2 9.0 - - + +
601D PHE* 3.6 17.5 - - + -
696D GLY 2.8 19.0 + - - +
697D GLN* 3.4 7.9 - - - +
699D ILE* 1.3 79.6 - - - +
701D TYR* 1.3 57.9 + - - +
703D ASP* 3.3 6.7 + - - +
704D SER* 2.8 28.6 + - - -
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Residues in contact with TYR 701 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601D PHE* 3.6 23.5 - + + -
611D THR* 6.1 0.7 - - - -
615D SER* 2.9 36.0 - - - -
680D LEU* 4.0 22.0 - - - +
683D SER* 5.5 4.0 + - - -
686D PHE* 5.4 8.9 + + + +
689D GLY 4.7 3.6 - - - -
690D VAL* 3.3 47.0 - - + +
692D PHE* 5.0 7.0 - + + -
697D GLN 2.9 17.2 + - - +
698D LEU* 3.7 5.4 - - + +
700D ALA* 1.3 76.4 - - - +
702D ILE* 1.3 61.1 + - + +
704D SER* 3.0 9.6 - - - -
705D LEU* 2.9 57.2 + - + +
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Residues in contact with ILE 702 (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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485D LYS* 5.4 6.3 - - + +
615D SER* 3.6 42.4 - - - +
618D SER* 3.6 21.5 - - - +
619D LEU* 3.9 26.4 - - + +
622D LEU* 4.3 17.5 - - + -
698D LEU* 3.0 27.1 + - + +
699D ILE* 3.6 8.1 - - - +
701D TYR* 1.3 76.8 - - + +
703D ASP* 1.3 65.5 + - - +
705D LEU* 2.9 10.7 + - + +
706D ASN* 2.9 20.3 + - - +
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Residues in contact with ASP 703 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488D THR* 4.8 6.9 - - - +
590D GLN 5.3 3.8 - - - +
591D MET 5.6 0.9 - - - +
593D PRO* 3.7 22.0 - - + +
596D PHE* 4.1 5.8 - - + -
622D LEU* 4.4 14.5 - - - +
626D HIS* 6.0 0.2 - - - -
699D ILE* 2.8 36.6 + - - +
700D ALA* 3.7 7.2 - - - +
702D ILE* 1.3 74.0 - - - +
704D SER* 1.3 62.7 + - - +
706D ASN* 3.2 11.6 + - - +
707D SER* 3.1 23.9 + - - -
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Residues in contact with SER 704 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596D PHE* 3.2 28.0 - - - -
601D PHE* 4.1 15.2 - - - -
700D ALA 2.8 14.2 + - - -
701D TYR* 3.0 24.8 - - - -
702D ILE 2.9 0.2 - - - -
703D ASP* 1.3 75.3 - - - +
705D LEU* 1.3 62.7 + - - +
707D SER* 3.1 15.4 + - - -
708D ASN* 3.3 18.5 + - - +
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Residues in contact with LEU 705 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615D SER* 4.2 18.6 - - - +
616D LEU* 5.4 0.7 - - - +
619D LEU* 4.2 22.4 - - + -
679D LEU* 4.4 25.4 - - + +
680D LEU* 5.1 7.9 - - + -
683D SER* 5.8 3.4 - - - +
701D TYR* 2.9 58.0 + - + +
702D ILE* 2.9 13.4 + - + +
704D SER* 1.3 76.8 - - - +
706D ASN* 1.3 62.7 + - - +
708D ASN* 3.2 22.0 + - - +
709D VAL* 3.1 24.4 + - - +
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Residues in contact with ASN 706 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591D MET 4.1 3.1 - - - +
593D PRO* 4.3 7.1 - - + +
619D LEU* 4.0 9.8 - - + +
622D LEU* 3.6 15.3 - - + +
623D LEU* 3.8 12.8 - - - +
626D HIS* 3.2 27.0 + - - -
702D ILE 2.9 11.2 + - - +
703D ASP* 3.2 18.9 - - - +
704D SER 3.1 0.2 - - - -
705D LEU* 1.3 77.3 - - - +
707D SER* 1.3 56.9 + - - +
709D VAL* 2.9 7.2 + - - +
710D TYR* 2.8 54.7 + - - -
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Residues in contact with SER 707 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593D PRO* 2.9 29.6 - - - +
594D GLY 4.0 4.3 + - - -
596D PHE* 3.3 20.6 - - - -
703D ASP 3.1 8.5 + - - -
704D SER 3.1 7.5 + - - -
706D ASN* 1.3 75.4 - - - +
708D ASN* 1.3 60.9 + - - +
710D TYR* 3.0 2.8 + - - +
711D ASN* 2.7 52.9 + - - +
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Residues in contact with ASN 708 (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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596D PHE* 5.3 2.4 - - - -
679D LEU* 4.8 12.3 + - + +
682D ASP* 4.0 25.3 + - - +
683D SER* 4.7 17.4 - - - +
704D SER* 3.3 16.9 + - - +
705D LEU* 3.2 25.5 + - - +
707D SER* 1.3 78.2 - - - +
709D VAL* 1.3 62.9 + - + +
711D ASN* 4.6 3.3 + - - +
712D ALA* 3.2 24.3 + - - +
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Residues in contact with VAL 709 (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 LEU* 4.4 10.1 - - + -
623D LEU* 3.9 22.2 - - + -
660D LYS* 3.6 25.9 - - + +
664D LEU* 4.1 38.1 - - + -
679D LEU* 4.5 12.1 - - + -
705D LEU 3.1 14.1 + - - +
706D ASN* 2.9 9.4 + - - +
708D ASN* 1.3 78.4 - - - +
710D TYR* 1.3 69.7 + - + +
711D ASN 3.5 0.3 + - - -
712D ALA* 3.6 11.9 + - - +
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Residues in contact with TYR 710 (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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591D MET* 3.7 11.3 - - - +
592D LYS* 4.5 12.9 - - + -
593D PRO* 3.9 16.6 - - + -
623D LEU* 3.3 14.7 - - + +
626D HIS* 2.6 31.5 + - - -
656D ASP* 4.7 0.2 - - - +
657D LEU* 3.4 41.9 - - + +
660D LYS* 3.0 32.6 + - + -
661D GLN* 3.0 30.5 + - + -
706D ASN* 2.8 38.2 + - - +
707D SER* 3.0 5.1 + - - +
709D VAL* 1.3 84.1 - - + +
711D ASN* 1.3 61.2 + - - +
712D ALA 3.4 0.2 - - - -
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Residues in contact with ASN 711 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
660D LYS* 4.9 0.7 - - - +
707D SER* 2.7 37.7 + - - +
708D ASN* 4.1 3.1 - - - +
710D TYR* 1.3 75.4 - - - +
712D ALA* 1.3 68.1 + - - +
713D SER* 3.5 1.7 + - - -
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Residues in contact with ALA 712 (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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660D LYS* 3.5 22.7 + - + -
682D ASP* 6.0 0.9 - - - +
708D ASN 3.2 18.7 + - - +
709D VAL* 3.8 11.4 - - - +
710D TYR 3.4 1.4 - - - -
711D ASN* 1.3 81.3 - - - +
713D SER* 1.3 68.3 + - - +
714D ILE* 5.4 3.1 - - + -
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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