Contacts of the helix formed by residues 651 - 664 (chain A) in PDB entry 2ADS
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 651 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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645A LYS* 4.1 4.5 - - - +
649A GLU 3.9 3.8 - - - +
650A LEU* 1.3 95.2 - - + +
652A VAL* 1.3 65.1 + - - +
653A GLU* 3.1 20.0 - - + +
654A VAL* 3.1 31.4 + - + +
655A LEU* 3.1 10.8 + - - +
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Residues in contact with VAL 652 (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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596A LEU* 6.2 0.7 - - + -
619A LYS* 3.3 24.2 - - + -
623A ASP* 4.2 20.2 - - + +
625A VAL* 4.3 16.8 - - + -
643A VAL* 5.7 1.6 - - + +
645A LYS* 3.6 39.0 - - + +
651A PRO* 1.3 72.2 - - - +
653A GLU* 1.3 77.3 + - - +
655A LEU* 3.6 8.4 - - - -
656A CYS* 2.8 42.5 + - - +
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Residues in contact with GLU 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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313A LYS* 5.4 1.4 + - - -
316A LEU* 3.6 25.3 - - + +
492A GLU* 5.1 3.1 - - - +
617A PHE* 5.7 9.3 - - + -
619A LYS* 3.8 16.0 - - - +
651A PRO* 3.3 20.4 - - + +
652A VAL* 1.3 96.1 - - - +
654A VAL* 1.3 58.9 + - + +
656A CYS* 3.4 3.5 + - - -
657A SER* 3.0 26.2 + - - -
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Residues in contact with VAL 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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492A GLU* 3.4 32.8 - - + +
493A GLY* 3.7 10.1 - - - +
650A LEU* 4.1 17.7 - - + -
651A PRO* 3.1 30.6 + - + +
653A GLU* 1.3 77.9 - - + +
655A LEU* 1.3 57.8 + - - +
657A SER* 3.1 10.0 + - - -
658A GLN* 3.0 41.4 + - - +
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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
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569A HIS* 4.4 1.2 + - - -
594A GLU* 3.4 38.6 - - + +
596A LEU* 3.9 29.4 - - + -
645A LYS* 3.6 22.2 - - + -
650A LEU* 3.6 25.8 - - + +
651A PRO 3.1 11.0 + - - +
652A VAL* 3.8 5.4 - - - +
654A VAL* 1.3 75.9 - - - +
656A CYS* 1.3 58.5 + - - +
658A GLN* 3.1 33.3 - - - +
659A ILE* 3.1 30.5 + - - +
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Residues in contact with CYS 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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316A LEU* 3.4 21.8 - - + -
625A VAL* 3.9 38.1 - - + -
627A LEU* 4.1 11.3 - - + +
643A VAL* 4.2 20.9 - - - -
652A VAL* 2.8 25.8 + - - +
653A GLU* 4.5 0.7 - - - -
655A LEU* 1.3 74.2 - - - +
657A SER* 1.3 59.5 + - - +
658A GLN 3.2 0.2 - - - -
659A ILE* 3.2 7.6 + - - +
660A LEU* 3.0 33.3 + - - +
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Residues in contact with SER 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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316A LEU* 3.7 5.3 - - - +
318A PHE* 3.6 32.4 - - - +
319A LYS* 4.3 2.9 - - - +
491A ILE* 4.6 0.2 - - - +
492A GLU* 3.4 40.8 + - - +
653A GLU 3.0 14.0 + - - -
654A VAL 3.1 9.8 + - - -
656A CYS* 1.3 75.6 - - - +
658A GLN* 1.3 54.5 + - - +
660A LEU 3.6 0.2 + - - -
661A SER* 3.0 31.3 + - - -
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Residues in contact with GLN 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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491A ILE* 4.1 6.0 - - + +
492A GLU 3.8 9.0 - - - +
493A GLY* 3.4 14.5 - - - -
495A VAL* 3.3 23.2 - - - +
498A PHE* 3.4 27.4 - - + -
567A VAL* 3.2 18.0 - - - +
569A HIS* 4.7 3.6 - - + -
650A LEU* 3.4 17.0 - - - +
654A VAL* 3.0 16.0 + - - +
655A LEU* 3.1 28.5 - - - +
656A CYS 3.2 0.2 - - - -
657A SER* 1.3 74.6 - - - +
659A ILE* 1.3 63.0 + - - +
661A SER* 3.4 8.2 - - - -
662A LEU* 3.2 28.4 + - - +
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Residues in contact with ILE 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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569A HIS* 3.2 33.0 - - + +
596A LEU* 4.6 2.2 - - + -
598A ILE* 4.4 10.5 - - + -
627A LEU* 3.8 12.6 - - + -
629A THR* 4.6 2.2 - - + -
641A ILE* 3.6 28.5 - - + -
643A VAL* 3.2 39.9 - - + -
655A LEU 3.1 15.2 + - - +
656A CYS* 3.2 8.5 + - - +
658A GLN* 1.3 74.4 - - - +
660A LEU* 1.3 65.7 + - - +
661A SER 3.1 0.7 + - - -
662A LEU* 3.3 11.1 + - - -
663A THR* 3.6 13.2 + - - +
676A PRO* 3.9 14.7 - - + +
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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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316A LEU* 3.9 23.3 - - + +
318A PHE* 3.1 57.6 - - + -
614A LYS* 3.8 25.1 + - + -
615A GLY* 3.9 6.5 - - - +
627A LEU* 4.1 16.6 - - + -
628A ALA 3.4 26.2 - - - +
629A THR* 4.6 2.9 - - + -
656A CYS 3.0 21.1 + - - +
657A SER 3.7 0.2 - - - +
659A ILE* 1.3 76.1 - - - +
661A SER* 1.3 55.7 + - - +
663A THR* 2.7 26.0 + - - -
664A LEU* 4.2 1.2 - - - +
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Residues in contact with SER 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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318A PHE* 3.6 5.6 - - - -
319A LYS* 4.0 12.6 + - - +
488A LEU* 3.5 13.2 - - - +
491A ILE* 2.9 48.1 - - - +
657A SER 3.0 17.8 + - - -
658A GLN 3.4 7.9 - - - -
660A LEU* 1.3 76.1 - - - +
662A LEU* 1.3 54.2 + - - +
664A LEU* 2.8 36.6 + - - +
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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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488A LEU* 4.5 0.2 - - - +
491A ILE* 5.7 4.3 - - + -
498A PHE* 3.8 19.5 - - + -
522A PHE* 4.3 23.1 - - + -
526A GLY* 4.4 13.7 - - - +
569A HIS* 3.5 30.7 - - + +
658A GLN 3.2 17.0 + - - +
659A ILE 3.3 0.8 + - - +
661A SER* 1.3 76.8 - - - +
663A THR* 1.3 60.7 + - - +
664A LEU 3.2 0.2 - - - -
665A MSE 3.1 19.3 + - + +
666A ASN* 3.4 0.3 + - - -
676A PRO* 3.9 16.6 - - + -
677A ALA* 3.1 42.4 + - + +
678A THR* 3.9 13.5 - - + +
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Residues in contact with THR 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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614A LYS* 2.9 22.5 + - - +
629A THR* 4.1 15.5 - - + -
659A ILE 3.6 13.9 + - - +
660A LEU 2.7 21.2 + - - +
661A SER 2.8 3.2 + - - -
662A LEU* 1.3 71.7 - - - +
664A LEU* 1.3 56.9 + - - +
666A ASN* 2.9 35.3 + - - +
667A TYR* 3.6 2.8 + - - -
668A SER* 4.7 2.9 + - - -
673A ILE* 4.6 12.6 - - - +
674A LYS 3.6 23.1 - - - +
675A LEU 4.6 1.1 - - - -
676A PRO* 3.7 16.4 - - + -
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Residues in contact with LEU 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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318A PHE* 4.2 8.1 - - + -
320A ASP* 4.1 33.0 - - + +
322A VAL* 4.6 1.6 - - + -
332A VAL* 4.0 21.1 - - + -
335A ASN* 4.3 0.4 - - - +
486A TYR* 4.0 35.2 - - + +
488A LEU* 4.1 18.9 - - + +
614A LYS* 3.5 28.3 - - - +
660A LEU 4.3 1.6 - - - +
661A SER 2.8 9.7 + - - +
663A THR* 1.3 74.1 - - - +
665A MSE 1.3 72.5 + - - +
666A ASN 3.8 0.2 - - - -
667A TYR* 4.1 8.8 - - - +
668A SER* 4.0 18.6 - - - -
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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