Contacts of the helix formed by residues 669 - 688 (chain B) in PDB entry 3QNF
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 669 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398B ASP* 5.8 0.2 - - - +
633B SER* 3.7 32.3 - - - +
636B ARG* 4.7 3.8 - - - +
667B GLU* 2.4 28.7 + - - +
668B THR* 1.3 91.2 + - - +
670B ILE* 1.3 67.5 + - - +
671B MET* 3.5 1.3 - - + +
672B PRO* 3.4 10.7 - - + +
673B VAL* 3.3 20.5 - - - +
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Residues in contact with ILE 670 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398B ASP* 4.6 17.4 + - - +
668B THR 4.0 0.6 + - - -
669B GLU* 1.3 76.5 + - - +
671B MET* 1.3 59.3 + - + +
673B VAL* 3.4 2.6 + - - +
674B PHE* 3.0 46.6 + - + -
723B SER* 4.7 10.8 - - - +
724B GLU* 5.1 7.6 - - + +
727B LEU* 4.1 24.5 - - + +
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Residues in contact with MET 671 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B GLY 5.9 0.2 - - - -
398B ASP* 3.3 47.3 + - - +
401B PHE* 4.5 7.2 - - + -
402B GLY* 4.3 12.1 - - - +
405B PHE* 3.6 35.4 - - + -
604B MET* 4.8 2.2 - - + -
633B SER* 5.2 2.7 - - - +
634B ASN* 4.2 14.4 - - - +
637B ALA* 3.9 13.0 - - + -
669B GLU* 4.7 0.8 - - + +
670B ILE* 1.3 77.3 - - - +
672B PRO* 1.3 69.1 - - + +
674B PHE* 3.4 14.3 + - + +
675B GLN* 3.1 28.8 + - - +
723B SER* 6.2 1.6 - - - -
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Residues in contact with PRO 672 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633B SER* 3.6 22.4 - - - +
636B ARG* 4.2 3.1 - - + +
637B ALA* 3.8 13.7 - - + +
640B ILE* 3.6 13.4 - - + +
663B TYR* 3.0 28.7 - - - +
664B LEU* 3.9 2.8 - - - +
667B GLU* 3.7 18.2 - - + +
669B GLU* 3.4 18.6 - - + +
671B MET* 1.3 95.9 - - + +
673B VAL* 1.3 55.3 + - - +
675B GLN* 3.3 3.4 + - + +
676B GLY* 2.8 24.1 + - - -
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Residues in contact with VAL 673 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664B LEU* 4.4 8.5 - - + +
667B GLU* 3.8 25.4 - - + +
669B GLU 3.3 16.4 - - - +
670B ILE* 3.4 7.7 + - - +
671B MET 3.3 0.4 - - - -
672B PRO* 1.3 74.3 - - - +
674B PHE* 1.3 54.8 + - - +
676B GLY* 3.0 2.9 + - - +
677B LEU* 2.7 45.4 + - + +
707B LEU* 4.1 24.1 - - + +
710B LEU* 4.8 10.3 - - + -
727B LEU* 3.5 27.4 - - + -
731B LEU* 4.8 6.3 - - + -
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Residues in contact with PHE 674 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
670B ILE* 3.0 26.3 + - + +
671B MET* 3.8 15.7 - - + +
672B PRO 3.4 0.2 - - - -
673B VAL* 1.3 74.9 - - - +
675B GLN* 1.3 59.0 + - + +
677B LEU* 3.3 9.0 + - + +
678B ASN* 2.8 44.6 + - - +
723B SER* 4.1 25.8 - - - -
726B MET* 3.6 24.0 - - + -
727B LEU* 3.3 46.2 - - + -
730B GLN* 4.7 9.0 - - + -
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Residues in contact with GLN 675 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B PHE* 3.3 41.8 - - + +
637B ALA* 3.8 20.4 - - + +
640B ILE* 4.1 18.7 - - + +
641B ASN* 3.5 26.6 + - - +
671B MET* 3.1 21.3 + - + +
672B PRO* 3.5 8.7 - - + +
674B PHE* 1.3 73.5 - - + +
676B GLY* 1.3 68.7 + - - +
678B ASN* 3.3 14.6 + - - +
679B GLU* 3.2 31.0 + - - +
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Residues in contact with GLY 676 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640B ILE* 4.0 9.5 - - - +
644B PHE* 5.8 0.7 - - - -
661B SER* 6.3 0.2 - - - -
664B LEU* 3.9 22.4 - - - -
672B PRO 2.8 15.0 + - - -
673B VAL 3.0 4.7 + - - -
675B GLN* 1.3 77.5 - - - +
677B LEU* 1.3 56.1 + - - +
679B GLU* 3.4 1.5 + - - +
680B LEU* 2.9 41.6 + - - +
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Residues in contact with LEU 677 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673B VAL* 2.7 37.0 + - + +
674B PHE* 3.8 12.8 - - + +
676B GLY* 1.3 74.7 - - - +
678B ASN* 1.3 61.0 + - - +
680B LEU* 4.6 0.9 - - - +
681B ILE* 2.9 54.9 + - + +
703B LEU* 4.4 8.5 - - + -
707B LEU* 3.0 32.5 - - + -
727B LEU* 4.5 9.0 - - + -
730B GLN* 4.8 13.9 - - + -
731B LEU* 4.2 13.5 - - + +
734B LEU* 3.8 16.2 - - + -
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Residues in contact with ASN 678 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
674B PHE* 2.8 34.5 + - - +
675B GLN* 3.3 17.8 + - - +
677B LEU* 1.3 75.5 - - - +
679B GLU* 1.3 64.7 + - + +
681B ILE* 5.4 0.2 - - - -
682B PRO* 3.2 21.8 - - - +
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Residues in contact with GLU 679 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640B ILE 5.0 3.1 - - - +
641B ASN* 4.2 7.7 + - - +
644B PHE* 3.4 48.6 - - + +
645B GLN* 3.0 33.2 - - - +
648B SER* 5.1 3.8 + - - -
675B GLN* 3.2 22.0 + - - +
676B GLY 4.2 1.1 - - - +
677B LEU 3.1 0.2 - - - -
678B ASN* 1.3 86.8 - - + +
680B LEU* 1.3 62.8 + - - +
681B ILE 3.6 0.4 - - - -
682B PRO* 3.8 5.9 - - - +
683B MET* 3.4 25.6 + - - +
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Residues in contact with LEU 680 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644B PHE* 3.8 20.0 - - + -
658B LEU* 3.6 31.2 - - + -
661B SER* 4.5 8.1 - - - -
664B LEU* 4.8 1.1 - - + -
676B GLY* 2.9 26.1 + - - +
677B LEU* 4.8 0.2 - - - -
679B GLU* 1.3 78.7 - - - +
681B ILE* 1.3 65.9 + - - +
683B MET* 3.1 21.6 + - - +
699B PHE* 3.4 24.2 - - + -
702B PHE* 4.4 9.6 - - + -
703B LEU* 3.8 32.5 - - + -
706B LEU* 4.0 20.2 - - + -
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Residues in contact with ILE 681 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677B LEU* 2.9 48.7 + - + +
678B ASN* 5.4 0.2 - - - -
680B LEU* 1.3 74.8 - - - +
682B PRO* 1.3 68.9 - - + +
683B MET 2.9 1.7 + - - -
684B TYR* 3.1 39.7 + - + +
685B LYS* 3.1 25.7 + - + +
703B LEU* 4.1 10.1 - - + -
730B GLN* 6.4 2.0 - - + -
734B LEU* 4.3 12.6 - - + -
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Residues in contact with PRO 682 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677B LEU 3.7 0.4 - - - +
678B ASN* 3.2 28.7 - - - +
679B GLU* 3.8 5.4 - - - +
680B LEU 3.6 2.9 - - - -
681B ILE* 1.3 95.9 - - + +
683B MET* 1.3 59.9 + - + +
685B LYS* 3.6 11.8 - - + +
686B LEU* 3.1 28.6 + - + +
881B GLN* 5.8 1.6 - - - +
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Residues in contact with MET 683 (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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644B PHE* 3.5 34.3 - - + -
647B VAL* 5.6 1.1 - - + -
654B ILE* 3.5 26.9 - - + -
658B LEU* 4.4 3.6 - - + -
679B GLU* 3.4 18.2 - - - +
680B LEU* 3.2 13.0 - - - +
681B ILE 2.9 1.0 + - - -
682B PRO* 1.3 74.6 - - + +
684B TYR* 1.3 64.9 + - - +
686B LEU* 3.2 9.2 + - - +
687B MET* 3.2 26.9 + - + +
699B PHE* 3.6 30.3 - - + -
921B TRP* 3.7 32.5 - - + +
929B ILE* 4.6 1.8 - - - -
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Residues in contact with TYR 684 (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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680B LEU 3.7 3.4 + - - -
681B ILE* 3.1 32.6 + - + +
683B MET* 1.3 77.4 - - - +
685B LYS* 1.3 79.4 + - + +
687B MET* 3.0 15.1 + - + +
688B GLU* 2.9 49.9 + - - +
696B GLU* 5.0 1.3 - - + +
699B PHE* 3.8 18.5 - + + -
700B LYS* 3.4 36.3 - - + -
703B LEU* 3.5 33.2 - - + -
734B LEU* 3.4 12.6 - - - +
737B VAL* 5.8 1.7 - - + +
738B HIS* 3.2 25.5 + + - -
807B ARG* 5.8 1.5 + - - -
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Residues in contact with LYS 685 (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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681B ILE* 3.1 19.2 + - + +
682B PRO* 3.6 15.5 - - + +
683B MET 3.2 0.2 - - - -
684B TYR* 1.3 98.3 + - + +
686B LEU* 1.3 58.1 + - - +
688B GLU* 2.9 36.2 + - - +
689B LYS* 3.5 23.4 + - - +
807B ARG* 3.4 25.7 - - - +
841B ARG* 3.2 26.3 + - - -
843B PRO* 4.4 1.0 - - - +
881B GLN* 3.3 37.9 - - - +
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Residues in contact with LEU 686 (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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682B PRO 3.1 15.5 + - - +
683B MET* 3.5 8.7 - - - +
684B TYR 3.1 0.2 - - - -
685B LYS* 1.3 75.4 - - - +
687B MET* 1.3 63.6 + - + +
688B GLU 3.2 2.7 - - - -
689B LYS* 3.3 16.8 + - - +
690B ARG* 4.1 9.7 + - - +
881B GLN* 3.1 41.1 - - + +
882B PHE 3.8 10.5 - - - +
883B SER* 4.0 17.0 - - - +
918B ASN* 3.8 28.0 - - + +
921B TRP* 4.2 29.4 - - + -
922B MET* 5.3 7.2 - - + -
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Residues in contact with MET 687 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683B MET* 3.2 17.1 + - + +
684B TYR* 3.0 16.7 + - - +
686B LEU* 1.3 71.6 - - - +
688B GLU* 1.3 64.9 + - - +
689B LYS 3.1 3.5 + - - -
690B ARG* 3.4 16.5 + - - +
692B MET* 4.0 28.3 - - - +
695B VAL* 3.4 32.5 - - + -
696B GLU* 3.5 31.7 - - + +
699B PHE* 4.0 17.7 - - + -
921B TRP* 5.5 2.7 - - + -
922B MET* 5.0 10.1 - - - -
926B PHE* 5.6 2.9 - - + -
929B ILE* 3.7 35.4 - - + -
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Residues in contact with GLU 688 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684B TYR* 2.9 27.5 + - - +
685B LYS* 2.9 47.3 + - - +
686B LEU 3.2 0.6 - - - -
687B MET* 1.3 78.4 - - - +
689B LYS* 1.3 65.8 + - + +
690B ARG 3.4 4.2 + - - +
696B GLU* 3.5 15.8 - - - +
700B LYS* 2.8 32.3 + - - +
807B ARG* 5.1 1.0 + - - -
841B ARG 3.8 4.5 - - - +
843B PRO* 3.7 30.6 - - + +
846B TYR* 3.3 20.6 + - - -
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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