Contacts of the helix formed by residues 662 - 684 (chain F) in PDB entry 2AJQ
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 THR 662 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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470F VAL* 4.5 6.5 - - - -
660F CYS* 3.2 8.4 - - - +
661F ARG* 1.3 107.8 - - + +
663F GLU* 1.3 61.8 - - - +
664F GLU* 3.1 23.5 + - - +
665F ILE* 3.1 26.6 + - + +
666F ALA 3.1 15.8 + - - -
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Residues in contact with GLU 663 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470F VAL* 4.2 17.7 - - + +
662F THR* 1.3 74.5 - - - +
664F GLU* 1.3 76.7 + - - +
665F ILE 3.2 0.2 - - - -
666F ALA* 3.4 6.4 - - - +
667F GLN* 3.0 23.6 + - - +
696F MET* 3.3 34.0 - - + +
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Residues in contact with GLU 664 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662F THR* 3.1 24.1 - - - +
663F GLU* 1.3 96.3 + - - +
665F ILE* 1.3 66.7 + - + +
667F GLN* 3.4 8.2 + - - +
668F VAL* 3.3 23.0 + - - +
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Residues in contact with ILE 665 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638F LEU* 4.2 24.7 - - + -
645F ASP* 3.6 34.3 - - + +
646F PHE* 4.3 3.1 - - + -
660F CYS* 3.8 14.1 - - + -
661F ARG* 3.8 27.8 - - + +
662F THR* 3.1 31.9 + - + +
664F GLU* 1.3 77.6 - - + +
666F ALA* 1.3 65.9 + - - +
668F VAL* 2.9 8.6 + - - +
669F VAL* 2.8 28.9 + - + +
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Residues in contact with ALA 666 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470F VAL* 4.6 3.4 - - + -
471F GLN 4.6 0.2 - - - +
472F ALA* 4.3 7.6 - - + +
660F CYS* 3.6 24.0 - - + +
662F THR 3.1 8.0 + - - +
663F GLU* 3.4 16.6 - - - +
665F ILE* 1.3 77.4 - - - +
667F GLN* 1.3 61.8 + - - +
669F VAL* 3.1 3.5 + - - +
670F ILE* 2.9 28.4 + - + +
696F MET* 3.6 28.0 - - + -
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Residues in contact with GLN 667 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663F GLU 3.0 14.0 + - - +
664F GLU* 3.7 10.5 - - - +
665F ILE 3.1 0.2 - - - -
666F ALA* 1.3 79.5 - - - +
668F VAL* 1.3 62.5 + - + +
670F ILE* 3.5 17.8 + - - +
671F GLU* 2.6 52.0 + - - +
696F MET* 3.9 19.2 - - + +
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Residues in contact with VAL 668 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633F LEU* 4.1 11.2 - - + -
636F LYS* 4.4 15.9 - - + +
638F LEU* 4.2 12.6 - - + -
664F GLU 3.3 11.8 + - - +
665F ILE* 2.9 11.6 + - - +
667F GLN* 1.3 76.8 - - + +
669F VAL* 1.3 60.9 + - - +
671F GLU* 3.4 12.2 + - - +
672F THR* 2.8 46.2 + - - +
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Residues in contact with VAL 669 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472F ALA* 4.3 6.3 - - + -
474F ILE* 3.7 21.5 - - + -
629F THR* 4.6 4.9 - - + +
633F LEU* 3.8 33.4 - - + -
638F LEU* 5.1 0.7 - - + -
646F PHE* 4.5 6.1 - - + -
648F TYR* 6.1 0.2 - - + -
658F VAL* 4.2 18.4 - - + -
660F CYS* 3.8 17.9 - - - -
665F ILE* 2.8 24.5 + - + +
666F ALA* 3.4 9.6 - - - +
668F VAL* 1.3 77.4 - - - +
670F ILE* 1.3 57.3 + - - +
672F THR* 3.3 2.1 + - - -
673F ALA* 2.9 29.3 + - - +
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Residues in contact with ILE 670 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472F ALA* 4.3 14.6 - - + -
474F ILE* 4.3 18.1 - - + +
666F ALA 2.9 20.1 + - - +
667F GLN* 3.8 18.8 - - - +
669F VAL* 1.3 76.2 - - - +
671F GLU* 1.3 63.0 + - + +
673F ALA* 3.4 3.3 + - - +
674F GLN* 3.3 20.1 + - - +
692F THR* 5.0 1.0 + - - -
694F GLY* 4.1 20.6 - - - +
695F LYS* 3.9 32.5 - - - +
696F MET* 4.3 17.5 - - + +
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Residues in contact with GLU 671 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636F LYS* 5.7 2.6 + - - +
667F GLN* 2.6 50.9 + - - +
668F VAL* 4.0 11.4 - - - +
670F ILE* 1.3 73.9 - - + +
672F THR* 1.3 65.5 + - - +
674F GLN* 3.2 8.6 + - - +
675F GLU* 3.0 29.3 + - + +
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Residues in contact with THR 672 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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629F THR* 3.8 11.4 - - + +
632F MET* 3.5 33.9 - - + -
633F LEU* 3.4 25.9 - - + +
636F LYS* 3.1 18.6 + - - +
668F VAL* 2.8 25.5 + - - +
669F VAL 3.6 3.8 - - - -
671F GLU* 1.3 76.6 - - - +
673F ALA* 1.3 58.4 + - - +
675F GLU* 2.9 13.8 + - - +
676F ALA* 2.9 27.2 + - - +
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Residues in contact with ALA 673 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474F ILE* 3.8 35.2 - - + -
625F TRP* 2.8 30.6 + - + +
629F THR* 3.6 19.5 - - + +
656F ILE* 4.9 0.4 - - + -
669F VAL 2.9 16.8 + - - +
670F ILE 3.6 6.1 - - - +
671F GLU 3.3 0.2 - - - -
672F THR* 1.3 76.5 - - - +
674F GLN* 1.3 61.6 + - - +
676F ALA 3.5 0.3 + - - -
677F MET* 3.1 10.9 + - - +
692F THR* 4.1 1.8 - - - -
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Residues in contact with GLN 674 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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670F ILE 3.3 8.5 + - - +
671F GLU* 3.2 11.3 + - - +
672F THR 3.1 0.4 - - - -
673F ALA* 1.3 77.2 - - - +
675F GLU* 1.3 64.8 + - + +
677F MET* 3.6 2.2 + - - +
678F ARG* 3.2 43.0 + - + +
691F ASP* 2.9 26.3 + - - -
692F THR* 2.7 51.3 + - - +
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Residues in contact with GLU 675 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632F MET* 3.6 22.5 - - + +
636F LYS* 2.8 34.4 + - - -
671F GLU* 3.0 18.4 + - + +
672F THR* 2.9 12.8 + - - +
674F GLN* 1.3 75.1 - - + +
676F ALA* 1.3 58.7 + - - +
678F ARG* 3.2 8.6 + - - +
679F TRP* 3.0 25.5 + - - +
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Residues in contact with ALA 676 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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625F TRP* 3.8 5.8 - - + -
628F LYS* 3.7 21.3 - - + -
629F THR* 3.4 31.2 - - - +
632F MET* 3.8 12.0 - - - -
672F THR 2.9 11.2 + - - +
673F ALA 3.8 1.1 - - - +
675F GLU* 1.3 75.4 - - - +
677F MET* 1.3 60.1 + - - +
679F TRP* 3.1 6.5 + - - +
680F VAL* 2.8 33.8 + - - +
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Residues in contact with MET 677 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476F ALA* 3.4 33.4 - - + -
479F LEU* 5.1 2.9 - - + -
621F ILE* 3.9 29.8 - - + -
622F CYS* 5.2 1.6 - - - -
625F TRP* 3.5 28.6 - - + -
673F ALA 3.1 10.7 + - - +
674F GLN* 3.9 4.7 - - - +
675F GLU 3.3 0.2 - - - -
676F ALA* 1.3 76.7 - - - +
678F ARG* 1.3 60.9 + - - +
680F VAL* 3.6 3.4 + - - +
681F GLY 3.2 15.2 + - - -
690F LEU* 3.7 34.6 - - + +
691F ASP 3.9 6.5 - - - +
692F THR* 3.5 33.2 - - + -
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Residues in contact with ARG 678 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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674F GLN* 3.2 29.0 + - + +
675F GLU* 3.2 9.3 + - - +
676F ALA 3.1 0.6 - - - -
677F MET* 1.3 74.4 - - - +
679F TRP* 1.3 65.8 + - - +
681F GLY* 3.2 2.9 + - - +
682F ASP* 3.1 23.1 + - - +
689F LEU* 3.5 42.9 - - - +
690F LEU* 3.2 18.2 - - - +
691F ASP* 2.6 30.5 + - - -
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Residues in contact with TRP 679 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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624F LEU* 3.8 36.3 - - + -
628F LYS* 3.4 44.4 - - + +
632F MET* 5.4 4.3 - - + -
675F GLU 3.0 14.0 + - - +
676F ALA* 3.1 12.8 + - - +
678F ARG* 1.3 76.5 - - - +
680F VAL* 1.3 77.6 + - + +
682F ASP* 2.9 8.8 + - - +
683F HIS* 2.8 67.9 + + + +
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Residues in contact with VAL 680 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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621F ILE* 4.1 27.4 - - + +
624F LEU* 3.9 21.3 - - + +
625F TRP* 3.8 30.3 - - + +
628F LYS* 4.6 1.3 - - + -
676F ALA 2.8 20.8 + - - +
677F MET* 3.8 8.1 - - - +
679F TRP* 1.3 93.7 - - + +
681F GLY* 1.3 62.8 + - - +
682F ASP 3.3 0.7 + - - -
683F HIS* 3.6 3.4 - - - +
684F TRP* 3.3 35.4 + - + +
686F PHE* 5.7 0.3 - - - -
690F LEU* 4.8 1.1 - - + -
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Residues in contact with GLY 681 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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677F MET 3.2 9.5 + - - -
678F ARG* 3.2 4.9 + - - -
679F TRP 3.2 0.4 - - - -
680F VAL* 1.3 80.1 - - - +
682F ASP* 1.3 56.9 - - - +
685F ASN 3.9 0.2 - - - -
686F PHE* 2.9 40.1 + - - +
688F CYS 5.6 0.2 - - - -
690F LEU* 3.9 23.8 - - - +
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Residues in contact with ASP 682 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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678F ARG 3.1 10.3 + - - +
679F TRP* 2.9 11.1 + - - +
681F GLY* 1.3 77.6 - - - +
683F HIS* 1.3 67.3 + - - +
684F TRP 3.3 0.4 - - - -
685F ASN* 3.2 19.8 + - - +
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Residues in contact with HIS 683 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212F GLU* 2.8 29.0 + - - -
624F LEU* 3.7 18.9 - - + +
679F TRP* 2.8 47.5 + + + +
680F VAL 3.6 5.2 - - - +
682F ASP* 1.3 79.7 - - - +
684F TRP* 1.3 73.7 + + - +
685F ASN* 3.3 7.8 + - - -
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Residues in contact with TRP 684 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212F GLU* 2.9 28.1 + - - -
216F ILE* 3.6 26.7 - - + -
486F HIS* 4.8 4.2 - - - -
596F LEU* 3.7 39.4 + - + -
597F ASP* 3.9 11.7 - - + -
620F LEU* 3.6 35.2 - - + -
621F ILE* 3.9 16.8 - - + -
624F LEU* 3.6 20.4 - - + -
680F VAL* 3.3 21.6 + - + +
682F ASP 3.3 0.4 - - - -
683F HIS* 1.3 94.7 - + - +
685F ASN* 1.3 74.1 + - - +
686F PHE* 3.0 17.0 + + + +
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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