Contacts of the helix formed by residues 663 - 682 (chain A) in PDB entry 4U6R
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 LEU 663 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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661A LEU 3.2 0.8 + - - -
662A GLY* 1.3 73.6 - - - -
664A GLU* 1.3 63.6 + - - +
665A PRO* 3.4 4.0 - - - -
666A ILE* 3.2 27.0 + - + +
667A THR* 3.1 25.0 + - - +
834A SER* 6.5 1.8 - - - -
1007A EDO 5.6 0.4 + - - -
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Residues in contact with GLU 664 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652A TYR* 2.7 31.4 + - + +
656A LYS* 5.1 1.7 + - - -
661A LEU* 3.1 22.3 + - - +
663A LEU* 1.3 76.9 - - - +
665A PRO* 1.3 65.8 - - - +
667A THR* 3.0 13.1 + - + -
668A LEU* 2.9 26.2 + - + +
703A GLY 4.6 2.9 - - - +
704A LYS* 5.3 1.0 - - - -
705A ILE* 3.3 36.9 + - + +
1007A EDO 3.2 37.0 + - - +
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Residues in contact with PRO 665 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652A TYR* 3.9 20.9 - - + +
658A PHE* 3.9 27.4 - - + -
661A LEU* 3.9 9.6 - - + +
662A GLY 3.6 12.6 - - - +
663A LEU 3.4 4.9 - - - -
664A GLU* 1.3 94.5 - - + +
666A ILE* 1.3 60.5 + - + +
668A LEU* 3.3 8.6 + - + +
669A LEU* 3.1 27.7 + - - +
767A VAL* 3.7 27.4 - - + +
768A ILE* 5.9 1.6 - - + -
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Residues in contact with ILE 666 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662A GLY 5.5 2.7 - - - +
663A LEU* 3.2 29.1 + - + +
664A GLU 3.2 0.6 - - - -
665A PRO* 1.3 78.9 - - + +
667A THR* 1.3 58.8 + - - +
669A LEU* 3.3 9.0 + - - +
670A GLN* 3.0 21.8 + - - +
768A ILE* 4.6 14.1 - - + -
831A PHE* 4.1 39.0 - - + +
832A PHE* 3.5 23.2 - - + -
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Residues in contact with THR 667 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663A LEU* 3.1 17.6 + - - +
664A GLU* 3.0 15.7 + - + -
666A ILE* 1.3 74.9 - - - +
668A LEU* 1.3 61.7 + - + +
670A GLN* 3.3 18.6 + - - +
671A GLN* 2.9 51.1 + - + +
705A ILE 5.7 1.1 - - - +
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Residues in contact with LEU 668 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649A LEU* 4.2 13.0 - - + -
652A TYR* 3.6 46.9 - - + +
664A GLU* 2.9 17.6 + - + +
665A PRO* 3.3 8.0 + - + +
667A THR* 1.3 77.8 - - + +
669A LEU* 1.3 55.2 + - + +
671A GLN* 3.5 19.0 + - - +
672A THR* 2.8 37.1 + - - -
696A ILE* 4.0 17.9 - - + -
705A ILE* 4.3 14.6 - - + +
706A LYS* 3.9 9.4 - - - -
707A ALA* 3.7 22.4 - - + +
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Residues in contact with LEU 669 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649A LEU* 4.8 3.8 - - + -
665A PRO 3.1 15.0 + - - +
666A ILE* 3.3 12.8 - - - +
667A THR 3.2 0.2 - - - -
668A LEU* 1.3 78.6 - - + +
670A GLN* 1.3 53.8 + - - +
672A THR* 3.5 6.2 + - - +
673A THR* 2.8 38.0 + - - -
763A VAL* 4.4 8.3 - - + +
764A PHE* 3.8 45.6 - - + +
767A VAL* 3.4 37.0 - - + -
768A ILE* 4.3 4.7 - - + -
831A PHE* 4.0 26.5 - - + -
832A PHE* 4.0 8.3 - - + -
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Residues in contact with GLN 670 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
666A ILE 3.0 9.1 + - - +
667A THR* 3.3 21.5 + - - +
669A LEU* 1.3 72.1 - - - +
671A GLN* 1.3 63.0 + - + +
673A THR* 3.5 3.6 + - - -
674A SER* 2.9 31.7 + - - -
827A LEU* 3.7 17.6 + - + +
832A PHE* 3.4 49.9 + - + +
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Residues in contact with GLN 671 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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624A ASN* 3.2 37.0 - - - +
667A THR* 2.9 37.7 + - + +
668A LEU* 3.5 15.4 - - - +
669A LEU 3.4 0.2 - - - -
670A GLN* 1.3 75.3 - - + +
672A THR* 1.3 61.3 + - - +
674A SER* 3.3 3.1 + - - -
675A GLY 2.9 24.6 + - - -
704A LYS* 6.3 0.8 - - - +
705A ILE 4.0 6.3 + - - -
706A LYS* 3.1 21.9 - - - +
707A ALA* 3.0 24.3 + - + +
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Residues in contact with THR 672 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624A ASN* 5.2 1.6 - - - -
649A LEU* 5.2 2.6 - - - +
668A LEU* 2.8 22.8 + - - +
669A LEU* 3.6 8.9 - - + -
671A GLN* 1.3 75.9 - - - +
673A THR* 1.3 59.1 + - - +
675A GLY 3.2 2.3 + - - -
676A LEU* 2.9 25.4 + - + +
689A LEU* 5.0 9.4 - - + -
694A ILE* 3.5 35.4 - - + +
707A ALA* 3.5 16.9 - - - +
709A ILE* 3.3 27.4 - - + +
760A ALA* 6.0 3.4 - - + -
763A VAL* 5.7 2.5 - - + -
764A PHE* 5.9 4.0 - - + -
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Residues in contact with THR 673 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669A LEU 2.8 20.3 + - - -
670A GLN* 3.7 5.8 - - - -
672A THR* 1.3 77.9 - - - +
674A SER* 1.3 57.0 + - - +
676A LEU* 3.3 13.3 + - + +
677A ALA* 2.8 27.0 + - - +
757A ILE* 6.2 0.4 - - + -
760A ALA* 5.6 1.6 - - - +
764A PHE* 3.2 24.7 - - + -
812A MET* 6.1 0.4 - - + -
823A ALA* 3.6 30.5 - - + +
826A VAL* 3.9 18.2 - - + -
827A LEU* 3.9 12.8 - - + -
832A PHE* 4.4 1.3 - - - -
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Residues in contact with SER 674 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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622A HIS* 3.3 25.7 + - - -
624A ASN* 3.8 5.4 + - - -
670A GLN* 2.9 20.8 + - - -
671A GLN* 3.4 8.1 - - - -
673A THR* 1.3 75.3 - - - +
675A GLY* 1.3 63.0 + - - +
677A ALA* 3.2 3.6 + - - +
678A HIS* 3.1 18.2 + - - +
827A LEU* 4.0 20.5 - - - +
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Residues in contact with GLY 675 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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622A HIS* 3.9 14.9 - - - -
624A ASN 3.8 20.9 - - - -
625A VAL* 4.0 3.9 - - - +
671A GLN 2.9 11.3 + - - -
672A THR 3.6 4.0 - - - -
674A SER* 1.3 74.9 - - - +
676A LEU* 1.3 60.5 + - - +
678A HIS* 3.3 4.9 + - - +
679A LEU* 3.1 26.5 + - - +
709A ILE* 3.9 6.1 - - - -
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Residues in contact with LEU 676 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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672A THR* 2.9 13.2 + - + +
673A THR* 3.3 15.7 - - + +
675A GLY* 1.3 74.9 - - - +
677A ALA* 1.3 59.0 + - - +
679A LEU* 3.3 7.6 + - + +
680A HIS* 3.0 57.5 + - + +
686A HIS* 4.5 10.3 - - + -
689A LEU* 3.9 23.1 - - + -
709A ILE* 3.5 12.0 - - + +
756A ASP* 3.8 34.3 - - + +
757A ILE* 4.3 13.0 - - + -
760A ALA* 4.5 7.6 - - + -
823A ALA* 4.5 4.0 - - + -
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Residues in contact with ALA 677 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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673A THR 2.8 19.0 + - - +
674A SER 3.2 6.4 + - - +
676A LEU* 1.3 71.3 - - - +
678A HIS* 1.3 65.9 + - - +
680A HIS* 3.4 4.0 + - - +
681A SER* 3.0 26.0 + - - -
823A ALA* 3.8 19.7 - - + +
824A LYS* 4.2 27.5 - - + -
827A LEU* 4.2 11.4 - - + -
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Residues in contact with HIS 678 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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619A SER* 2.9 31.9 + - - -
621A GLU* 4.2 19.5 - - + +
622A HIS* 3.5 45.1 - + + +
625A VAL* 4.2 5.2 - - + -
674A SER 3.1 7.6 + - - +
675A GLY 3.4 9.0 - - - +
677A ALA* 1.3 77.0 - - - +
679A LEU* 1.3 64.4 + - + +
681A SER* 2.6 26.8 + - - -
682A LEU* 3.3 33.2 + - + +
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Residues in contact with LEU 679 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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619A SER* 4.0 22.0 - - - -
625A VAL* 3.7 30.3 - - + -
675A GLY 3.1 7.5 + - - +
676A LEU* 3.6 13.5 - - + +
678A HIS* 1.3 81.3 - - + +
680A HIS* 1.3 64.7 + - + +
682A LEU* 3.0 15.0 + - - +
683A ASN 3.5 0.2 + - - -
684A ILE* 3.0 44.8 + - + +
686A HIS* 4.4 18.8 - - + -
709A ILE* 4.2 15.5 - - + -
712A PHE* 3.8 25.1 - - + -
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Residues in contact with HIS 680 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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676A LEU* 3.0 36.3 + - + +
677A ALA* 3.9 6.1 - - - +
678A HIS 3.3 0.2 - - - -
679A LEU* 1.3 77.3 - - + +
681A SER* 1.3 57.0 + - - +
683A ASN* 3.1 16.5 + - - -
684A ILE 3.2 20.6 - - - -
753A TYR* 3.5 43.5 + + + +
756A ASP* 2.8 33.3 + - + +
757A ILE* 4.5 8.5 - - + -
823A ALA* 4.3 11.3 + - + +
1008A EPE 3.3 39.5 + - - -
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Residues in contact with SER 681 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677A ALA 3.0 15.3 + - - -
678A HIS* 2.6 26.5 + - - -
680A HIS* 1.3 75.5 - - - +
682A LEU* 1.3 63.4 + - - +
683A ASN* 3.4 1.6 - - - +
824A LYS* 4.6 15.9 - - - -
1008A EPE 3.1 28.9 + - - -
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Residues in contact with LEU 682 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618A GLU* 3.5 30.3 - - + +
619A SER* 3.7 15.0 - - - -
678A HIS* 3.3 35.9 + - + +
679A LEU* 3.0 9.5 + - - +
681A SER* 1.3 83.7 + - - +
683A ASN* 1.3 67.8 + - - +
684A ILE* 3.3 18.5 + - + +
717A LYS* 3.9 14.0 + - - +
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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