Contacts of the helix formed by residues 653 - 670 (chain A) in PDB entry 4N41
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 653 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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544A LEU* 3.8 28.3 - - + -
573A VAL* 4.8 3.1 - - + -
605A THR* 6.1 0.7 - - + -
617A LEU* 4.5 6.7 - - + -
635A ILE* 3.6 35.4 - - + +
638A LEU* 3.7 11.2 - - + -
639A THR* 3.7 13.2 - - - +
651A ARG 4.3 2.5 - - - +
652A LEU* 1.3 95.6 - - + +
654A ALA* 1.3 67.9 + - - +
655A PRO 3.1 2.6 - - - -
656A LEU* 3.1 25.2 + - + -
657A HIS 3.2 5.7 + - - -
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Residues in contact with ALA 654 (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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494A VAL* 4.8 5.4 - - + -
501A LEU* 5.1 1.8 - - + -
638A LEU 2.9 21.9 + - - +
639A THR* 4.2 0.4 - - - +
641A LEU* 3.9 19.5 - - + -
642A TYR* 4.2 18.2 - - + +
650A PRO* 6.1 0.2 - - - -
652A LEU 3.5 2.5 + - - -
653A PRO* 1.3 69.8 - - - +
655A PRO* 1.3 70.4 - - + +
657A HIS* 4.2 7.6 - - - -
658A LEU* 2.9 40.5 + - + +
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Residues in contact with PRO 655 (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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474A ALA* 3.7 21.1 - - + +
475A VAL 4.1 0.4 - - - -
476A GLY* 3.4 29.0 - - - +
492A CYS* 3.5 16.9 - - + +
493A ALA 5.0 0.2 - - - +
494A VAL* 3.7 24.0 - - + -
544A LEU* 4.3 7.6 - - + -
638A LEU* 4.2 7.6 - - + -
653A PRO* 3.4 12.8 - - + -
654A ALA* 1.3 93.1 - - + +
656A LEU* 1.3 56.0 + - - +
658A LEU* 4.3 7.9 - - + -
659A ALA* 2.9 28.8 + - - +
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Residues in contact with LEU 656 (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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476A GLY* 3.6 9.9 - - - -
477A PHE 3.8 15.9 - - - +
478A ASP* 4.9 3.0 - - + +
544A LEU* 3.4 40.4 - - + +
545A ARG* 4.1 7.6 - - - +
546A ASP* 4.7 1.8 - - + +
573A VAL* 3.6 42.4 - - + +
652A LEU* 4.3 15.9 - - + +
653A PRO* 3.1 19.1 + - + +
655A PRO* 1.3 76.9 - - - +
657A HIS* 1.3 61.7 + - - +
658A LEU 3.3 0.2 - - - -
659A ALA* 3.9 3.4 - - + +
660A ASP* 2.9 31.5 + - - +
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Residues in contact with HIS 657 (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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642A TYR* 3.5 34.1 - + + -
650A PRO* 3.8 27.5 - - + +
652A LEU* 4.1 23.2 - - + +
653A PRO 3.2 9.5 + - - +
654A ALA* 3.8 11.9 - - - +
656A LEU* 1.3 77.0 - - - +
658A LEU* 1.3 63.4 + - - +
660A ASP* 3.2 8.6 - - - +
661A ARG* 3.0 54.1 + - - +
4C G 2.7 23.6 + - - -
5C G 4.1 17.0 + - - -
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Residues in contact with LEU 658 (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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492A CYS* 3.6 26.9 - - + -
493A ALA 5.2 1.8 - - - +
494A VAL* 5.4 0.2 - - + -
501A LEU* 4.0 34.1 - - + -
502A LEU 5.6 1.1 - - - +
642A TYR* 3.4 29.8 - - + -
654A ALA* 2.9 30.9 + - + +
655A PRO* 4.3 2.2 - - + -
657A HIS* 1.3 76.6 - - - +
659A ALA* 1.3 57.7 + - - +
661A ARG* 3.0 5.0 + - - -
662A LEU* 2.9 25.1 + - - +
682A LEU* 4.1 15.9 - - + -
684A PHE* 3.4 24.3 - - + -
685A VAL* 4.0 9.0 - - + -
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Residues in contact with ALA 659 (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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476A GLY 3.7 20.2 - - - +
477A PHE 4.5 0.2 - - - -
478A ASP* 3.7 20.0 - - + -
490A ALA 4.3 5.2 - - - +
491A ALA* 4.4 0.7 - - - -
492A CYS* 3.6 15.0 - - - +
655A PRO 2.9 20.0 + - - +
656A LEU* 3.9 5.4 - - - +
657A HIS 3.4 0.2 - - - -
658A LEU* 1.3 75.2 - - - +
660A ASP* 1.3 58.5 + - - +
662A LEU* 3.6 3.9 - - - +
663A VAL* 2.9 35.2 + - - +
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Residues in contact with ASP 660 (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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478A ASP* 3.9 21.5 - - - +
575A LYS* 3.0 33.0 + - - -
652A LEU* 3.9 8.6 - - + +
656A LEU 2.9 17.4 + - - +
657A HIS* 3.2 10.1 - - - +
659A ALA* 1.3 77.4 - - - +
661A ARG* 1.3 71.2 + - - +
663A VAL* 3.3 2.6 + - - +
664A LYS* 3.0 39.7 + - - +
6D T 4.2 7.8 + - - -
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Residues in contact with ARG 661 (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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642A TYR* 3.9 19.7 - - - +
657A HIS* 3.0 34.5 + - - +
658A LEU* 3.6 7.6 - - - +
660A ASP* 1.3 84.9 - - - +
662A LEU* 1.3 56.7 + - - +
664A LYS* 3.3 34.8 + - + +
665A GLU* 2.9 33.5 + - + +
684A PHE* 3.9 26.7 - - + +
685A VAL* 4.8 5.8 - - - +
4C G 2.8 45.9 + - - -
5C G 5.0 4.9 + - - -
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Residues in contact with LEU 662 (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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490A ALA* 3.6 25.6 - - + -
491A ALA 3.9 0.4 - - - +
492A CYS* 3.9 10.1 - - - -
503A TRP* 3.9 24.0 - - + -
504A THR 3.9 10.8 - - - +
505A LEU* 4.1 8.5 - - + -
658A LEU 2.9 13.1 + - - +
659A ALA* 3.6 7.6 - - - +
660A ASP 3.2 0.2 - - - -
661A ARG* 1.3 73.0 - - - +
663A VAL* 1.3 65.9 + - - +
665A GLU* 3.1 1.9 + - - -
666A VAL* 2.9 38.4 + - + +
683A PHE* 3.6 33.2 - - + -
684A PHE* 3.6 22.2 - - + -
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Residues in contact with VAL 663 (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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478A ASP* 3.5 37.7 - - + +
480A GLY* 3.5 29.2 - - - +
482A ARG* 4.7 7.9 - - - +
489A GLY* 4.2 4.0 - - - -
490A ALA* 3.6 24.0 - - + +
659A ALA 2.9 13.0 + - - +
660A ASP 3.9 1.6 - - - +
662A LEU* 1.3 75.9 - - - +
664A LYS* 1.3 65.8 - - - +
666A VAL* 3.3 7.7 + - + +
667A GLY* 3.0 20.1 + - - -
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Residues in contact with LYS 664 (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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660A ASP* 3.0 28.6 + - - +
661A ARG* 3.4 44.6 - - + +
662A LEU 3.2 0.2 - - - -
663A VAL* 1.3 78.4 - - - +
665A GLU* 1.3 58.3 + - + +
667A GLY* 3.2 3.8 + - - -
668A ARG* 2.9 66.8 + - - +
7D A 3.7 30.4 + - - +
8D C 6.1 1.3 - - - +
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Residues in contact with GLU 665 (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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418A ARG* 2.9 34.0 + - - -
422A LYS* 4.6 2.3 - - - +
661A ARG* 2.9 21.1 + - + +
662A LEU 3.1 2.0 + - - +
664A LYS* 1.3 73.9 - - + +
666A VAL* 1.3 61.5 + - - +
668A ARG* 2.8 32.5 + - - +
669A LEU* 2.9 51.2 + - + +
671A ILE* 5.1 0.2 - - - -
683A PHE* 4.6 9.6 - - + -
684A PHE* 3.5 38.8 - - + +
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Residues in contact with VAL 666 (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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505A LEU* 3.6 33.2 - - + -
662A LEU* 2.9 30.3 + - + +
663A VAL* 3.6 8.3 - - + +
665A GLU* 1.3 74.7 - - - +
667A GLY* 1.3 63.7 + - - +
670A GLY* 3.1 21.1 + - - -
671A ILE* 3.4 39.5 + - + +
683A PHE* 5.1 1.1 - - + -
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Residues in contact with GLY 667 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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663A VAL 3.0 14.2 + - - -
664A LYS 3.6 3.8 - - - -
666A VAL* 1.3 80.1 - - - +
668A ARG* 1.3 61.7 + - - +
669A LEU 3.4 0.5 + - - -
670A GLY* 3.9 5.2 + - - -
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Residues in contact with ARG 668 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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415A TRP* 3.4 44.5 - - + +
418A ARG* 3.9 19.3 - - - +
419A ASN* 3.5 30.7 + - - +
664A LYS* 2.9 54.0 + - - +
665A GLU* 2.8 32.3 + - - +
667A GLY* 1.3 78.1 - - - +
669A LEU* 1.3 60.8 + - - +
1C T 5.3 6.1 - - - -
8D C 5.6 5.3 + - - -
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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
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418A ARG* 4.2 5.8 - - - +
419A ASN* 3.4 44.4 - - - +
422A LYS* 4.0 23.6 - - + -
423A ALA* 3.9 24.6 - - + +
426A LEU* 4.1 25.6 - - + -
427A ARG* 4.9 4.2 + - - -
665A GLU* 2.9 31.7 + - + +
668A ARG* 1.3 81.5 - - - +
670A GLY* 1.3 62.2 + - - +
671A ILE* 4.7 9.3 - - + +
683A PHE* 5.2 4.7 - - + -
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Residues in contact with GLY 670 (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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666A VAL 3.1 9.6 + - - -
667A GLY 3.9 4.5 + - - -
668A ARG 3.7 1.2 - - - -
669A LEU* 1.3 80.6 - - - +
671A ILE* 1.3 63.6 + - - +
672A ARG* 3.7 4.9 + - - +
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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
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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