Contacts of the helix formed by residues 652 - 671 (chain A) in PDB entry 5OQN
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 ASN 652 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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616A PRO* 4.1 26.5 - - - +
620A GLU* 5.2 0.2 - - - +
650A LYS 3.8 1.2 + - - -
651A GLY* 1.3 74.0 - - - +
653A ALA* 1.3 59.6 + - - +
654A SER* 4.3 8.4 + - - +
655A LEU* 3.0 27.7 + - - +
656A LYS* 2.6 34.7 + - - +
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Residues in contact with ALA 653 (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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652A ASN* 1.3 73.9 - - - +
654A SER* 1.3 55.4 + - - +
656A LYS* 3.6 4.6 - - - +
657A TYR* 2.6 39.0 + - - +
699A LEU* 3.8 40.7 - - + +
701A GLU* 5.1 5.6 - - + +
702A CYS* 4.1 6.6 - - - -
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Residues in contact with SER 654 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616A PRO* 6.0 0.4 - - - -
620A GLU* 2.8 32.5 - - - +
652A ASN* 3.3 8.1 + - - -
653A ALA* 1.3 78.1 - - - +
655A LEU* 1.3 62.3 + - - +
657A TYR* 3.2 11.0 + - - +
658A ILE* 3.1 22.3 + - - +
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Residues in contact with LEU 655 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616A PRO* 6.3 1.6 - - + -
619A ARG* 3.1 46.4 - - + +
620A GLU* 4.0 15.0 + - + +
623A VAL* 3.7 29.8 - - + -
647A CYS* 4.1 24.2 - - + +
651A GLY* 4.4 8.7 - - - -
652A ASN* 3.0 20.9 + - - +
654A SER* 1.3 76.5 - - - +
656A LYS* 1.3 61.2 + - - +
657A TYR 3.1 0.3 + - - -
658A ILE* 3.1 11.6 + - + +
659A ALA* 2.8 30.9 + - + +
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Residues in contact with LYS 656 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647A CYS 3.9 9.3 + - - +
648A VAL* 2.8 41.5 - - + +
649A SER 4.4 9.4 + - - +
650A LYS 4.9 0.4 - - - -
651A GLY 2.5 26.5 + - - +
652A ASN* 2.6 22.4 + - - +
653A ALA* 3.7 3.1 - - - +
655A LEU* 1.3 74.2 - - - +
657A TYR* 1.3 62.9 + - - +
659A ALA* 4.5 0.2 - - - -
660A LEU* 3.3 23.1 + - + +
693A VAL* 4.9 9.9 - - + -
696A ASN* 5.0 7.5 - - - +
699A LEU* 3.7 29.8 - - - +
702A CYS* 4.9 10.4 - - + +
705A ILE* 5.0 0.2 - - - +
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Residues in contact with TYR 657 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653A ALA 2.6 23.5 + - - +
654A SER* 3.2 10.5 - - - +
655A LEU 3.1 0.2 - - - -
656A LYS* 1.3 76.6 - - - +
658A ILE* 1.3 71.6 + - + +
661A GLN* 3.2 46.9 + - - +
701A GLU* 4.5 27.8 - - + -
702A CYS* 4.3 8.7 - - - -
705A ILE* 3.3 42.0 - - + +
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Residues in contact with ILE 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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620A GLU* 4.1 34.3 - - + +
623A VAL* 4.6 3.6 - - + -
624A LYS* 4.3 33.2 - - + +
654A SER 3.1 10.0 + - - +
655A LEU* 3.2 22.4 - - + +
657A TYR* 1.3 85.4 - - + +
659A ALA* 1.3 70.3 + - - +
661A GLN* 3.3 26.6 + - - +
662A VAL* 3.3 15.3 + - + +
514B ILE* 4.6 11.4 - - + -
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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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623A VAL* 4.2 16.4 - - + -
644A LEU* 4.5 5.6 - - + +
647A CYS* 4.2 18.6 - - + -
648A VAL* 3.5 22.0 - - + +
655A LEU* 2.8 23.1 + - + +
656A LYS 4.1 0.9 - - - +
658A ILE* 1.3 81.2 - - - +
660A LEU* 1.3 63.9 + - - +
662A VAL* 3.2 13.2 + - - +
663A ILE* 3.3 15.9 + - - +
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Residues in contact with LEU 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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648A VAL* 3.8 20.8 - - + +
656A LYS* 3.3 16.8 + - + +
657A TYR 4.0 3.6 - - - +
658A ILE 3.3 0.2 - - - -
659A ALA* 1.3 79.0 - - - +
661A GLN* 1.3 64.1 + - - +
663A ILE* 3.0 24.0 + - + +
664A VAL* 3.1 22.2 + - + +
689A ILE* 5.4 3.4 - - + -
690A PHE* 3.7 29.4 - - + -
693A VAL* 3.8 32.5 - - + -
702A CYS* 4.2 2.9 - - + +
705A ILE* 4.4 10.5 - - + -
706A ALA* 3.8 26.5 - - + +
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Residues in contact with GLN 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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657A TYR* 3.2 50.9 + - - +
658A ILE* 3.3 17.5 + - - +
660A LEU* 1.3 75.4 - - - +
662A VAL* 1.3 63.9 + - - +
664A VAL* 3.2 14.6 + - - +
665A ASP* 3.2 19.5 + - - -
705A ILE* 3.8 23.4 - - + +
513B PHE* 3.3 49.3 - - + +
514B ILE* 4.3 9.6 - - + +
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Residues in contact with VAL 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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623A VAL* 3.9 28.5 - - + +
624A LYS* 4.9 2.7 - - - -
627A GLY* 3.4 29.2 - - - +
644A LEU* 4.1 17.9 - - + -
658A ILE* 3.4 14.6 - - + +
659A ALA 3.2 8.2 + - - +
660A LEU 3.2 0.6 - - - -
661A GLN* 1.3 75.8 - - - +
663A ILE* 1.3 62.9 + - - +
665A ASP* 3.1 3.8 + - - +
666A ILE* 2.9 43.2 + - + +
514B ILE* 4.5 20.8 - - + +
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Residues in contact with ILE 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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641A MET* 4.2 12.1 - - + +
644A LEU* 4.0 32.1 - - + -
645A GLY* 4.4 6.5 - - - +
648A VAL* 3.8 28.9 - - + -
659A ALA 3.5 8.7 - - - +
660A LEU* 3.0 15.7 + - + +
662A VAL* 1.3 74.8 - - - +
664A VAL* 1.3 63.9 + - - +
666A ILE* 3.5 8.1 + - - +
667A PHE* 3.1 51.4 + - + -
686A LEU* 4.8 14.1 - - + -
689A ILE* 5.8 2.5 - - + -
690A PHE* 4.9 12.3 - - + -
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Residues in contact with VAL 664 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
660A LEU* 3.1 26.8 + - + +
661A GLN* 3.2 7.1 + - - +
663A ILE* 1.3 77.4 - - - +
665A ASP* 1.3 56.8 + - - +
667A PHE* 3.3 6.8 + - - +
668A SER* 3.1 27.1 + - - +
690A PHE* 4.6 14.6 - - + -
705A ILE 4.7 3.4 - - - +
709A GLY* 3.6 34.1 - - - +
712A LYS* 4.4 8.7 - - + +
713A LEU* 3.7 21.0 - - + +
513B PHE* 3.7 21.5 - - + -
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Residues in contact with ASP 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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631A LEU* 3.6 16.2 - - + -
661A GLN 3.2 8.3 + - - +
662A VAL 3.1 7.6 + - - +
664A VAL* 1.3 74.1 - - - +
666A ILE* 1.3 66.1 + - - +
667A PHE 3.1 1.6 - - - -
668A SER* 2.9 17.4 + - - -
669A VAL* 3.2 17.0 + - - +
712A LYS* 3.8 7.6 + - - -
512B LEU* 3.8 15.1 - - + +
513B PHE* 3.0 28.7 + - - +
514B ILE* 2.9 44.8 + - + +
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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
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627A GLY 5.0 0.9 - - - +
630A CYS* 3.9 26.2 - - + -
631A LEU* 3.7 14.1 - - + +
637A ALA* 3.8 23.1 - - + -
641A MET* 4.1 21.5 - - - -
644A LEU* 3.8 19.5 - - + -
662A VAL* 2.9 42.2 + - + +
663A ILE* 3.8 6.5 - - - +
665A ASP* 1.3 75.7 - - - +
667A PHE* 1.3 57.7 + - + +
670A HIS* 3.1 35.4 + - + +
674A VAL* 4.2 9.6 - - + +
514B ILE* 6.5 0.2 - - + -
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Residues in contact with PHE 667 (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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641A MET* 4.1 7.0 - - + -
663A ILE* 3.1 41.1 + - + -
664A VAL 3.5 7.9 - - - +
665A ASP 3.1 0.6 - - - -
666A ILE* 1.3 79.3 - - + +
668A SER* 1.3 63.3 + - - +
671A GLY* 2.7 57.5 + - - -
672A ASN* 4.3 5.2 - - - -
674A VAL* 4.3 4.3 - - + -
675A VAL* 3.6 38.4 - - + -
683A SER* 6.2 1.1 - - - -
686A LEU* 3.8 15.3 - - + -
690A PHE* 5.4 2.0 - + - -
713A LEU* 4.0 21.5 - - + -
718A VAL* 4.3 9.5 - - + +
719A PHE* 4.0 32.3 - + - -
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Residues in contact with SER 668 (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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664A VAL* 3.1 17.0 + - - +
665A ASP* 2.9 14.2 + - - -
667A PHE* 1.3 77.5 - - - +
669A VAL* 1.3 61.5 + - - +
671A GLY 4.8 0.3 + - - -
712A LYS* 4.7 0.3 + - - -
713A LEU* 4.0 10.0 - - - +
718A VAL* 5.5 5.2 - - - +
512B LEU* 4.0 17.5 - - - +
520B MET* 3.1 46.2 - - - +
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Residues in contact with VAL 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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631A LEU* 3.8 30.3 - - + +
665A ASP 3.2 15.6 + - - +
667A PHE 3.1 0.4 - - - -
668A SER* 1.3 82.3 - - - +
670A HIS* 1.3 74.1 + - + +
671A GLY 3.6 0.4 - - - -
512B LEU* 4.3 18.8 - - + -
518B GLN* 4.9 16.6 - - - +
520B MET* 6.4 0.2 - - + -
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Residues in contact with HIS 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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630A CYS 3.1 25.8 + - - -
631A LEU* 3.6 20.7 + - - -
632A LEU 5.1 2.0 - - - -
633A ASP 4.6 0.2 - - - -
634A VAL* 4.0 27.6 - - + +
637A ALA* 4.6 4.7 - - + -
666A ILE* 3.1 37.1 + - + +
669A VAL* 1.3 89.6 + - + +
671A GLY* 1.3 63.2 + - - +
673A THR* 3.0 39.4 + - - +
674A VAL* 4.0 13.0 - - + -
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Residues in contact with GLY 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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667A PHE* 2.7 49.8 + - - -
668A SER 4.6 0.8 + - - -
669A VAL 3.6 0.8 - - - -
670A HIS* 1.3 73.5 - - - +
672A ASN* 1.3 64.6 + - - -
673A THR 3.7 0.3 + - - -
674A VAL* 3.8 7.1 - - - +
718A VAL* 4.0 17.7 - - - -
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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