Contacts of the helix formed by residues 656 - 675 (chain D) in PDB entry 1DQA
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 GLY 656 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D NAP 2.6 22.6 + - - -
588D MET* 3.9 4.9 - - - -
651D SER* 4.0 18.8 - - - -
654D ALA* 3.0 4.1 - - - -
655D MET* 1.3 78.7 - - - +
657D MET* 1.3 53.6 + - - +
659D MET* 4.3 2.5 - - - -
660D ILE* 2.7 38.3 + - - +
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Residues in contact with MET 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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4D NAP 3.4 51.8 + - + +
588D MET* 4.0 9.8 - - + +
589D THR 3.2 28.5 - - - +
590D ARG* 3.5 28.5 - - - +
655D MET* 3.5 21.5 - - + -
656D GLY* 1.3 74.5 - - - +
658D ASN* 1.3 57.9 + - - +
660D ILE* 4.4 4.3 - - + -
661D SER* 2.8 36.2 + - - +
690D ASP* 3.6 10.8 - - - +
702D ARG* 3.2 16.8 - - - +
770D GLN* 3.9 6.3 - - - +
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Residues in contact with ASN 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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863C VAL* 4.8 0.7 - - - +
866C HIS* 3.3 26.2 + - - +
867C MET* 3.9 15.4 - - + +
870C ASN* 3.0 35.6 + - - +
871C ARG* 3.9 2.2 + - - +
4D NAP 2.9 61.8 + - - +
657D MET* 1.3 77.5 - - - +
659D MET* 1.3 55.6 + - - +
661D SER* 3.2 6.6 + - - -
662D LYS* 3.0 30.5 + - - +
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Residues in contact with MET 659 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
871C ARG* 3.6 12.5 - - - +
4D NAP 2.9 48.7 + - - +
625D THR* 4.6 3.1 + - - -
626D SER* 3.7 11.6 - - - +
628D PHE* 4.0 2.2 - - + -
629D ALA* 3.6 38.2 - - + +
651D SER* 3.7 26.5 - - - +
654D ALA* 3.6 31.2 - - + -
656D GLY 3.6 3.8 - - - +
658D ASN* 1.3 76.7 - - - +
660D ILE* 1.3 61.7 + - + +
662D LYS* 3.4 5.9 + - - +
663D GLY* 3.1 19.8 + - - -
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Residues in contact with ILE 660 (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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588D MET* 4.0 19.3 - - + +
589D THR* 3.9 15.3 - - - +
590D ARG* 3.4 28.3 - - + +
622D PHE* 3.7 10.8 - - + -
629D ALA* 4.5 1.6 - - + -
647D PHE 4.9 2.7 - - - +
649D SER* 3.9 21.8 - - - +
650D ARG 3.9 11.2 - - - +
651D SER* 3.8 26.0 - - - -
656D GLY 2.7 25.5 + - - +
657D MET* 4.1 3.6 - - + +
659D MET* 1.3 78.0 - - + +
661D SER* 1.3 60.0 + - - +
663D GLY 3.4 0.3 + - - -
664D THR* 2.8 34.2 + - - +
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Residues in contact with SER 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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862C LEU* 5.2 3.1 - - - -
863C VAL* 3.7 21.3 - - - +
4D NAP 3.1 20.8 + - - -
590D ARG* 3.1 23.3 + - - -
657D MET 2.8 24.2 + - - -
658D ASN* 3.2 6.0 + - - -
660D ILE* 1.3 75.8 - - - +
662D LYS* 1.3 57.4 + - - +
664D THR* 3.2 7.8 + - - -
665D GLU* 2.9 29.6 + - - +
683D VAL* 4.2 6.1 - - - +
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Residues in contact with LYS 662 (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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863C VAL* 3.9 20.3 - - + +
867C MET* 3.9 26.3 - - + +
871C ARG* 3.9 22.8 - - - +
4D NAP 5.7 0.8 + - - -
625D THR* 3.9 31.0 + - + +
658D ASN 3.0 16.0 + - - +
659D MET* 3.7 6.1 - - - +
661D SER* 1.3 75.5 - - - +
663D GLY* 1.3 64.6 + - - +
665D GLU* 3.3 9.6 + - - +
666D LYS* 3.2 21.7 + - - +
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Residues in contact with GLY 663 (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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622D PHE* 3.4 33.8 - - - -
625D THR* 3.4 21.0 + - - -
659D MET 3.1 13.6 + - - -
660D ILE 3.4 2.7 + - - -
662D LYS* 1.3 75.6 - - - +
664D THR* 1.3 57.2 + - - +
666D LYS* 3.3 2.1 + - - +
667D ALA* 2.9 24.4 + - - +
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Residues in contact with THR 664 (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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590D ARG* 3.4 20.9 - - + +
592D PRO* 3.7 34.5 - - + -
622D PHE* 3.5 15.0 - - - -
647D PHE* 3.8 15.1 - - + -
660D ILE* 2.8 23.7 + - - +
661D SER 3.2 5.4 + - - -
663D GLY* 1.3 74.8 - - - +
665D GLU* 1.3 60.2 + - - +
667D ALA* 3.2 2.9 + - - +
668D LEU* 2.8 43.0 + - + +
683D VAL* 4.1 8.7 - - + -
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Residues in contact with GLU 665 (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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860C GLY 4.4 13.0 - - - +
863C VAL* 3.8 34.5 + - + +
864C LYS* 4.6 12.9 + - - +
661D SER 2.9 16.2 + - - +
662D LYS* 3.3 9.0 + - - +
664D THR* 1.3 76.2 - - - +
666D LYS* 1.3 61.7 + - - +
668D LEU* 3.5 7.0 + - - +
669D SER* 3.1 22.7 + - - -
680D ILE* 5.6 0.3 - - - +
683D VAL* 4.5 11.1 - - + +
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Residues in contact with LYS 666 (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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621D ALA* 3.5 19.7 - - + +
624D SER* 3.0 31.8 + - - +
625D THR* 3.6 26.9 - - + +
662D LYS 3.2 7.2 + - - +
663D GLY 3.8 2.5 - - - +
665D GLU* 1.3 75.5 - - - +
667D ALA* 1.3 65.0 + - - +
669D SER* 3.2 8.5 + - - -
670D LYS* 3.0 24.1 + - + +
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Residues in contact with ALA 667 (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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618D ILE* 3.8 25.6 - - + +
621D ALA* 4.1 10.7 - - - +
622D PHE* 4.1 6.1 - - + -
647D PHE* 3.6 30.7 - - + -
663D GLY 2.9 17.6 + - - +
664D THR 3.2 2.2 + - - +
666D LYS* 1.3 76.0 - - - +
668D LEU* 1.3 57.4 + - - +
670D LYS* 3.3 3.8 + - - +
671D LEU* 2.9 27.8 + - - +
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Residues in contact with LEU 668 (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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592D PRO* 3.7 36.1 - - + -
594D VAL* 4.0 20.9 - - + -
645D ILE* 4.3 9.6 - - + -
647D PHE* 4.2 13.2 - - + -
664D THR* 2.8 30.0 + - + +
665D GLU* 3.8 6.5 - - - +
667D ALA* 1.3 72.4 - - - +
669D SER* 1.3 60.1 + - - +
671D LEU* 3.2 10.5 + - + +
672D HIS* 2.9 30.3 + - - +
678D MET* 3.6 4.2 - - + +
680D ILE* 3.9 35.6 - - + +
683D VAL* 4.6 9.2 - - + -
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Residues in contact with SER 669 (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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665D GLU* 3.1 14.6 + - - -
666D LYS* 3.2 14.1 + - - -
668D LEU* 1.3 76.6 - - - +
670D LYS* 1.3 61.6 + - - +
672D HIS* 3.3 8.9 + - - +
673D GLU* 3.3 29.6 + - - +
680D ILE* 4.4 6.2 - - - +
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Residues in contact with LYS 670 (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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617D VAL* 4.4 9.2 - - + +
618D ILE* 4.3 9.9 - - + -
620D GLU* 6.0 2.0 - - - -
621D ALA* 3.8 25.8 - - + +
666D LYS* 3.0 14.6 + - + +
667D ALA 3.5 8.1 - - - +
668D LEU 3.2 0.2 - - - -
669D SER* 1.3 75.2 + - - +
671D LEU* 1.3 65.8 + - - +
673D GLU* 2.9 42.7 + - - +
674D TYR* 3.3 34.6 - - + +
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Residues in contact with LEU 671 (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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605D VAL* 4.3 11.4 - - + -
608D TRP* 3.5 33.4 - - + -
609D LEU* 4.1 12.6 - - + -
618D ILE* 4.1 7.6 - - + +
645D ILE* 3.8 27.4 - - + -
647D PHE* 6.0 1.6 - - + -
667D ALA 2.9 17.8 + - - +
668D LEU* 3.6 11.4 - - + +
670D LYS* 1.3 76.9 - - - +
672D HIS* 1.3 56.2 + - - +
674D TYR* 3.0 8.3 + - - +
675D PHE* 2.9 41.1 + - + +
678D MET* 3.6 26.2 - - + -
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Residues in contact with HIS 672 (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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668D LEU 2.9 16.4 + - - +
669D SER* 3.5 9.8 + - - +
671D LEU* 1.3 76.0 - - - +
673D GLU* 1.3 61.1 + - - +
675D PHE 2.9 30.2 - - - -
676D PRO* 2.9 38.3 + - + +
678D MET* 2.9 38.9 + - + +
680D ILE* 4.6 9.9 - - + -
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Residues in contact with GLU 673 (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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669D SER* 3.3 20.9 + - - +
670D LYS* 2.9 44.9 + - + +
672D HIS* 1.3 80.4 - - + +
674D TYR* 1.3 63.3 + - + +
676D PRO* 4.0 7.6 - - - +
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Residues in contact with TYR 674 (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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608D TRP* 3.5 36.3 - + + -
617D VAL* 3.6 37.0 - - + +
670D LYS* 3.3 39.7 + - + +
671D LEU* 3.0 7.7 + - - +
673D GLU* 1.3 80.2 - - + +
675D PHE* 1.3 84.4 + + + +
676D PRO* 3.5 6.5 - - - +
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Residues in contact with PHE 675 (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 LEU* 4.7 7.9 - - + -
604D GLU* 4.2 25.4 - - + -
605D VAL* 3.7 33.7 - - + -
608D TRP* 3.8 48.2 - + + -
671D LEU* 2.9 24.7 + - + +
672D HIS* 2.9 10.3 - - - +
674D TYR* 1.3 99.7 - + + +
676D PRO* 1.3 60.1 - - - +
677D GLU 3.2 2.9 - - - +
678D MET* 3.0 34.7 + - + +
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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
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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