Contacts of the helix formed by residues 666 - 680 (chain A) in PDB entry 5N4D
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 PRO 666 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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657A VAL* 3.6 25.1 - - + -
658A ASN 5.9 0.7 - - - +
659A ILE* 3.6 21.1 - - + -
664A VAL 3.9 5.4 - - - +
665A VAL* 1.3 86.0 - - + +
667A MET* 1.3 66.6 + - - +
668A HIS 3.0 3.6 + - - -
669A SER* 3.1 7.8 + - - +
670A PHE* 2.9 49.8 + - + -
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Residues in contact with MET 667 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LEU 3.4 27.4 - - - +
41A GLU* 3.7 21.8 - - + +
606A ASP* 4.1 12.8 - - + +
609A LYS* 4.5 4.0 - - + +
613A PHE* 3.7 31.4 - - + -
665A VAL* 4.0 12.8 - - + +
666A PRO* 1.3 80.5 - - - +
668A HIS* 1.3 97.8 + - + +
670A PHE* 3.6 5.8 - - - -
671A LYS* 2.9 55.1 + - - +
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Residues in contact with HIS 668 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603A GLY 3.2 17.5 - - - +
604A VAL* 3.8 10.1 - - + +
605A ALA* 3.1 17.4 + - - +
606A ASP* 3.0 45.0 + - - +
610A PHE* 3.6 23.9 + - + +
619A TRP* 4.9 2.6 - - - -
641A VAL* 4.3 0.2 - - - +
664A VAL* 3.3 18.1 - - + +
665A VAL* 3.3 34.3 + - + +
666A PRO 3.0 0.6 - - - -
667A MET* 1.3 99.3 - - + +
669A SER* 1.3 57.7 + - - +
671A LYS* 3.9 2.1 - - - +
672A PHE* 3.0 29.1 + - - +
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Residues in contact with SER 669 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584A MET* 4.4 5.9 - - - +
602A GLY* 4.4 2.6 - - - -
603A GLY 4.0 21.0 + - - -
655A ILE* 3.7 21.0 - - - +
657A VAL* 3.5 33.4 - - - +
666A PRO* 3.1 6.7 + - - +
668A HIS* 1.3 77.7 - - - +
670A PHE* 1.3 64.7 + - - +
672A PHE* 3.8 6.3 - - - +
673A ILE* 3.0 26.2 + - - +
689A ILE* 4.0 2.0 - - - +
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Residues in contact with PHE 670 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LEU* 3.7 35.0 - - + -
42A GLU 5.8 0.4 - - - -
47A VAL* 4.4 9.4 - - + -
50A TRP* 3.7 29.1 - + + -
51A THR* 3.6 25.4 - - + -
657A VAL* 4.5 3.8 - - + -
659A ILE* 5.1 1.8 - - + -
666A PRO* 2.9 48.9 + - + +
667A MET* 3.8 7.2 - - - +
668A HIS 3.2 0.2 - - - -
669A SER* 1.3 76.5 - - - +
671A LYS* 1.3 57.9 + - - +
673A ILE* 3.3 3.7 - - - +
674A ALA* 2.9 29.8 + - - +
689A ILE* 3.8 11.9 - - + -
691A ILE* 4.0 25.4 - - + -
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Residues in contact with LYS 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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35A ASP* 2.8 29.0 + - - +
37A TYR* 3.6 32.3 - - + +
40A LEU* 4.3 10.1 - - + -
41A GLU* 2.8 33.0 + - - -
606A ASP* 2.8 31.6 + - + +
609A LYS* 3.7 2.4 - - - +
641A VAL* 4.2 15.5 - - + -
667A MET* 2.9 35.8 + - + +
668A HIS* 4.0 2.5 - - - +
670A PHE* 1.3 73.1 - - - +
672A PHE* 1.3 63.5 + - - +
674A ALA* 3.8 1.7 - - - +
675A THR* 2.8 32.1 + - - +
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Residues in contact with PHE 672 (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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584A MET* 3.4 48.2 - - + -
587A ILE* 4.3 11.4 - - + -
588A VAL* 3.8 13.5 - - + -
605A ALA* 3.9 8.1 - - + -
640A PRO* 3.6 45.3 - - + -
641A VAL* 3.9 7.8 - - + +
644A VAL* 3.9 9.6 - - + -
653A THR* 5.5 0.7 - - + -
655A ILE* 3.8 14.6 - - + -
668A HIS 3.0 19.5 + - - +
669A SER 3.8 3.4 - - - +
670A PHE 3.2 0.2 - - - -
671A LYS* 1.3 77.9 - - - +
673A ILE* 1.3 57.3 + - - +
675A THR* 3.3 4.1 + - - -
676A LEU* 2.9 53.6 + - + +
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Residues in contact with ILE 673 (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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50A TRP* 3.7 21.3 - - + -
54A GLN* 5.1 0.2 - - - -
653A THR* 5.2 0.9 - - + -
655A ILE* 3.8 24.0 - - + -
669A SER 3.0 16.2 + - - +
670A PHE 3.3 10.5 - - - +
672A PHE* 1.3 75.5 - - - +
674A ALA* 1.3 69.3 + - - +
676A LEU* 3.3 9.7 + - + +
677A GLN* 2.9 42.0 + - - +
687A LEU* 3.7 37.0 - - + +
688A LEU 3.9 5.4 - - - +
689A ILE* 3.9 24.5 - - + -
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Residues in contact with ALA 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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14A THR* 4.0 12.9 - - + -
37A TYR* 3.7 35.8 + - + -
40A LEU* 3.9 9.2 - - + -
50A TRP* 4.2 5.6 - - + -
670A PHE 2.9 18.4 + - - +
671A LYS 3.8 3.4 - - - +
673A ILE* 1.3 78.9 - - - +
675A THR* 1.3 57.4 + - - +
677A GLN* 3.7 6.7 - - - +
678A HIS* 2.9 30.0 + - - +
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Residues in contact with THR 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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37A TYR* 3.7 19.8 - - + -
641A VAL* 3.8 30.4 - - - +
644A VAL* 3.8 15.7 - - + -
671A LYS* 2.8 24.6 + - - -
672A PHE* 3.7 5.6 - - - -
674A ALA* 1.3 75.6 - - - +
676A LEU* 1.4 59.8 + - - +
678A HIS* 3.7 1.5 - - + +
679A ASN* 2.9 55.5 + - - +
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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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587A ILE* 4.7 7.6 - - + -
588A VAL* 5.3 0.9 - - + -
644A VAL* 3.9 30.5 - - + +
650A MET* 4.2 26.5 - - + -
653A THR* 4.8 4.9 - - + -
672A PHE* 2.9 48.9 + - + +
673A ILE* 3.7 22.9 - - + +
675A THR* 1.4 76.4 - - - +
677A GLN* 1.3 58.1 + - - +
680A VAL* 2.9 38.0 + - + +
687A LEU* 4.1 24.0 - - + -
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Residues in contact with GLN 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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11A TYR* 3.3 50.9 - - + +
12A PRO 4.5 2.9 - - - +
14A THR* 4.7 3.6 + - - -
54A GLN* 2.9 42.0 + - - -
57A LEU* 5.1 0.4 - - - +
673A ILE* 2.9 31.1 + - + +
674A ALA* 4.0 4.8 - - - +
676A LEU* 1.3 77.1 - - - +
678A HIS* 1.3 60.5 + - - +
680A VAL 4.9 0.9 - - - -
681A PRO* 3.4 25.4 - - - +
687A LEU* 2.9 30.4 + - + +
688A LEU* 4.7 0.6 - - - +
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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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16A ARG* 3.3 51.9 + - - +
37A TYR* 3.1 18.6 + + + +
674A ALA 2.9 11.4 + - - +
675A THR* 3.7 4.3 - - - +
676A LEU 3.2 0.2 - - - -
677A GLN* 1.3 78.4 - - - +
679A ASN* 1.3 79.5 + - - +
681A PRO* 3.4 11.6 - - - +
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Residues in contact with ASN 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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644A VAL* 3.7 32.1 + - + +
645A ARG 3.7 6.7 - - - +
646A THR* 3.3 37.4 - - + +
675A THR* 2.9 45.4 + - - +
676A LEU 4.2 0.2 - - - +
678A HIS* 1.3 96.2 - - - +
680A VAL* 1.3 64.6 + - - +
681A PRO* 3.4 4.7 - - - +
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Residues in contact with VAL 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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11A TYR* 4.8 0.5 - - - -
644A VAL* 5.6 0.9 - - + -
645A ARG 3.7 17.5 - - - +
646A THR 3.8 14.8 - - - +
648A LYS 3.9 17.0 - - - +
650A MET* 4.3 12.6 - - + -
676A LEU* 2.9 25.1 + - + +
679A ASN* 1.3 82.4 - - + +
681A PRO* 1.3 67.0 - - - +
682A GLN 3.2 2.7 - - - +
683A ASN* 2.9 30.9 + - + +
687A LEU* 3.8 21.1 - - + +
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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
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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