Contacts of the helix formed by residues 558 - 572 (chain C) in PDB entry 3DXD
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 GLY 558 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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557C VAL* 1.3 79.0 - - - +
559C VAL* 1.3 66.2 + - - -
560C ASP* 3.2 15.3 - - - -
561C VAL* 3.0 13.2 + - - +
562C ILE* 3.2 10.9 + - - +
611C PHE* 3.5 22.6 - - - -
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Residues in contact with VAL 559 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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616A ARG* 5.8 2.5 - - - +
558C GLY* 1.3 67.9 - - - -
560C ASP* 1.3 70.6 + - + +
562C ILE* 3.5 7.3 - - + +
563C ASN* 3.0 37.5 + - - +
611C PHE* 3.7 7.3 - - + -
613C ALA* 4.0 9.2 - - + -
616C ARG* 4.1 16.2 - - - +
678D GLN 3.6 21.3 - - - +
679D GLN 3.7 14.6 - - - +
680D ASN* 3.8 28.0 - - - +
681D GLY 3.8 3.4 - - - +
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Residues in contact with ASP 560 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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616A ARG* 3.5 50.6 + - - +
679B GLN* 6.1 1.3 - - - +
555C LYS* 4.4 12.5 + - - +
557C VAL 4.6 0.3 - - - +
558C GLY* 3.4 17.0 - - - -
559C VAL* 1.3 78.9 + - + +
561C VAL* 1.3 70.2 + - - +
564C GLY* 2.9 25.6 + - - -
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Residues in contact with VAL 561 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553C VAL* 3.6 33.1 - - + +
554C ALA* 5.0 1.3 - - + +
555C LYS* 4.1 25.6 - - + +
557C VAL 3.5 22.2 - - - +
558C GLY 3.0 7.7 + - - +
560C ASP* 1.3 88.7 - - - +
562C ILE* 1.3 61.2 + - - +
564C GLY* 3.2 2.8 + - - -
565C ALA* 2.9 27.1 + - - +
624C ILE* 3.8 16.2 - - + -
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Residues in contact with ILE 562 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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558C GLY 3.2 5.5 + - - +
559C VAL* 3.5 12.3 - - - +
561C VAL* 1.3 74.8 - - - +
563C ASN* 1.3 91.4 + - - +
565C ALA* 3.1 8.5 + - - +
566C LEU* 2.8 38.2 + - + +
611C PHE* 4.0 10.3 - - + -
613C ALA* 3.8 31.4 - - + +
614C VAL 4.2 0.4 - - - +
615C GLY* 4.0 16.2 - - - +
622C ALA* 3.8 25.1 - - + +
624C ILE* 3.7 32.8 - - + +
634C CYS* 4.1 3.1 - - - -
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Residues in contact with ASN 563 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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563A ASN* 5.3 1.6 - - + -
567A GLU* 2.5 26.2 - - - +
616A ARG* 3.9 18.8 - - + +
559C VAL* 3.0 31.0 + - - +
560C ASP* 4.7 0.2 - - - -
562C ILE* 1.3 84.9 - - - +
564C GLY* 1.3 65.2 + - - +
566C LEU* 4.0 1.3 - - - +
567C GLU* 3.0 32.3 + - - +
614C VAL 4.9 1.0 + - - -
615C GLY* 3.4 6.2 - - - -
616C ARG* 3.1 46.6 + - + +
678D GLN 4.9 0.8 + - - -
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Residues in contact with GLY 564 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616A ARG* 3.4 27.7 - - - +
617A ASP* 4.2 4.1 - - - +
560C ASP 2.9 14.3 + - - -
561C VAL* 3.2 4.4 + - - -
563C ASN* 1.3 76.9 - - - +
565C ALA* 1.3 60.6 + - - +
567C GLU* 3.8 2.1 - - - +
568C SER* 3.1 23.8 + - - -
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Residues in contact with ALA 565 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551C VAL* 3.7 20.6 - - + +
553C VAL* 4.0 8.0 - - + +
561C VAL 2.9 12.9 + - - +
562C ILE 3.1 7.6 + - - +
564C GLY* 1.3 75.7 - - - +
566C LEU* 1.3 55.9 + - - +
568C SER* 3.3 7.4 + - - -
569C VAL* 2.9 25.1 + - - +
634C CYS* 3.7 17.3 - - - -
636C MET* 3.4 24.1 - - - +
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Residues in contact with LEU 566 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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567A GLU* 3.9 10.1 - - - +
548C LEU* 4.4 10.5 - - + -
562C ILE* 2.8 30.1 + - + +
563C ASN* 3.8 9.4 - - - +
564C GLY 3.3 0.2 - - - -
565C ALA* 1.3 69.8 - - - +
567C GLU* 1.3 59.6 + - - +
569C VAL* 3.3 1.1 + - - +
570C LEU* 2.8 40.7 + - + +
615C GLY* 3.8 17.9 - - - +
620C THR* 3.4 42.6 - - + +
621C PHE 4.3 6.1 - - - +
622C ALA* 4.6 5.6 - - + -
636C MET* 3.5 32.3 - - + -
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Residues in contact with GLU 567 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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563A ASN* 2.6 43.0 - - - +
566A LEU* 3.9 10.4 - - - +
567A GLU* 3.5 19.4 - - + +
570A LEU* 3.6 20.8 - - + +
615A GLY 3.9 1.7 - - - -
616A ARG* 3.2 8.9 + - - +
617A ASP* 3.1 34.5 + - + +
620A THR* 3.9 5.1 + - + -
638A TRP* 5.0 0.2 - - - -
563C ASN 3.0 20.1 + - - +
564C GLY 3.8 3.1 - - - +
566C LEU* 1.3 74.2 - - - +
568C SER* 1.3 63.1 + - - +
570C LEU* 4.6 1.3 - - - -
571C SER* 3.0 26.0 + - - -
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Residues in contact with SER 568 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617A ASP* 3.5 20.6 + - - -
551C VAL* 5.5 8.0 - - - +
564C GLY 3.1 14.3 + - - -
565C ALA* 3.5 10.5 - - - -
567C GLU* 1.3 77.1 - - - +
569C VAL* 1.3 61.4 + - - +
571C SER* 2.7 21.0 + - - -
572C SER* 3.3 9.5 + - - -
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Residues in contact with VAL 569 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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548C LEU* 3.4 52.3 - - + +
549C GLY* 5.2 1.3 - - - -
551C VAL* 5.0 10.2 - - + +
565C ALA 2.9 10.7 + - - +
566C LEU* 3.6 9.0 - - - +
568C SER* 1.3 77.5 - - - +
570C LEU* 1.3 64.6 + - - +
572C SER* 3.3 16.3 + - - +
573C SER* 3.0 26.0 + - - +
636C MET* 3.8 32.5 - - + -
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Residues in contact with LEU 570 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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567A GLU* 3.7 37.5 - - + +
570A LEU* 3.3 29.9 - - + +
571A SER* 3.7 20.6 - - - -
573A SER 4.8 0.3 - - - +
548C LEU* 4.1 19.3 - - + -
566C LEU* 2.8 30.7 + - + +
567C GLU 4.0 1.3 - - - +
569C VAL* 1.3 74.6 - - + +
571C SER* 1.3 60.3 + - - +
573C SER* 3.2 19.9 - - - +
578C TRP* 3.8 22.7 - - + +
620C THR* 4.4 14.8 - - + -
638C TRP* 4.2 4.9 - - + -
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Residues in contact with SER 571 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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570A LEU* 4.0 17.6 - - - +
573A SER 5.6 0.3 - - - +
574A SER* 5.5 1.0 - - - -
575A ARG* 3.1 42.6 + - - +
578A TRP* 3.9 6.6 - - - -
638A TRP* 3.4 31.5 - - - -
567C GLU 3.0 15.1 + - - -
568C SER* 2.7 20.4 + - - -
570C LEU* 1.3 77.2 - - - +
572C SER* 1.3 57.6 + - - +
573C SER 3.6 2.6 + - - +
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Residues in contact with SER 572 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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575A ARG* 4.1 16.8 - - - +
568C SER 3.3 14.3 + - - -
569C VAL* 3.3 12.5 + - - +
570C LEU 3.3 1.2 - - - -
571C SER* 1.3 78.3 + - - +
573C SER* 1.3 59.7 + - - +
577C GLN* 4.3 6.2 + - - +
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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