Contacts of the helix formed by residues 561 - 575 (chain A) in PDB entry 1DQ8
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 CYS 561 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A COA 3.8 39.4 - - + +
560A GLY* 1.3 75.2 - - - +
562A LEU* 1.3 58.6 + - - +
563A VAL 3.3 2.2 - - - -
564A ALA* 4.2 3.4 - - - -
565A SER* 2.7 32.4 + - - -
528B GLU* 2.6 26.0 + - - -
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Residues in contact with LEU 562 (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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100A COA 3.4 15.8 - - + -
555A MET* 5.3 3.4 - - - -
557A THR* 3.7 28.5 - - + +
559A GLU* 3.4 21.9 + - + +
560A GLY 3.2 4.9 + - - -
561A CYS* 1.3 77.9 - - - +
563A VAL* 1.3 58.8 + - + +
565A SER* 3.7 1.1 - - - -
566A THR* 2.8 43.0 + - - +
752A HIS* 3.9 19.7 - - + -
755A ASN* 3.7 45.8 - - + +
756A ILE* 4.1 5.8 - - + -
759A ALA* 4.2 7.4 - - + -
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Residues in contact with VAL 563 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A COA 5.5 0.2 - - + -
539A GLY* 4.3 4.5 - - - -
540A VAL 3.6 23.1 - - - +
555A MET* 3.4 34.2 - - + +
557A THR* 3.9 24.5 - - + -
559A GLU 4.8 0.4 + - - +
562A LEU* 1.3 73.0 - - + +
564A ALA* 1.3 61.9 + - - +
566A THR* 3.2 1.6 + - - -
567A ASN* 2.8 32.4 + - - +
527B CYS* 4.0 17.3 - - - -
528B GLU* 3.3 31.0 + - + +
529B ASN* 4.2 2.9 - - + +
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Residues in contact with ALA 564 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A COA 3.6 61.9 + - + +
561A CYS* 3.7 8.3 - - - +
563A VAL* 1.3 75.8 - - - +
565A SER* 1.3 58.4 + - - +
567A ASN* 3.4 2.8 + - - +
568A ARG* 2.9 28.1 + - - +
528B GLU* 2.9 22.3 + - + +
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Residues in contact with SER 565 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A COA 2.9 50.6 + - - +
561A CYS 2.7 21.9 + - - -
562A LEU* 3.7 4.0 - - - -
564A ALA* 1.3 70.9 - - - +
566A THR* 1.3 65.6 + - - +
568A ARG 3.2 0.7 + - - -
569A GLY 3.0 8.8 + - - -
752A HIS* 4.7 2.6 - - - -
849A GLY* 4.4 3.3 + - - -
852A SER* 2.8 44.0 + - - -
853A LEU 3.8 0.9 + - - -
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Residues in contact with THR 566 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541A ALA* 4.1 5.8 - - + -
555A MET* 3.9 17.7 - - - -
562A LEU* 2.8 25.3 + - - +
563A VAL 3.8 3.1 - - - -
565A SER* 1.3 75.0 - - - +
567A ASN* 1.3 57.9 + - - +
569A GLY* 3.3 1.6 + - - -
570A CYS* 2.9 29.1 + - - -
752A HIS* 5.4 0.3 - - - -
756A ILE* 3.9 17.4 - - + +
845A THR* 3.4 44.0 - - + +
848A ALA* 3.8 3.1 - - + +
849A GLY* 4.4 11.7 - - - +
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Residues in contact with ASN 567 (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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100A COA 3.0 44.2 + - + +
540A VAL 4.3 2.7 + - - +
541A ALA* 3.5 11.1 - - + +
542A GLY* 2.8 44.1 + - - +
563A VAL 2.8 18.2 + - - +
564A ALA 3.5 5.4 - - - +
566A THR* 1.3 77.5 - - - +
568A ARG* 1.3 62.2 + - - +
570A CYS* 3.3 4.8 + - - +
571A ARG* 3.1 17.8 + - - +
479B TYR* 4.4 5.0 - - - -
529B ASN* 3.9 12.2 + - - +
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Residues in contact with ARG 568 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A COA 3.2 91.2 + - + +
564A ALA 2.9 15.0 + - - +
565A SER 3.2 3.3 + - - +
567A ASN* 1.3 74.9 - - - +
569A GLY* 1.3 65.1 + - - +
571A ARG* 3.1 12.3 + - - +
572A ALA* 3.1 10.6 + - - +
720A VAL* 3.3 16.0 + - + +
721A LEU* 3.2 31.0 + - + +
722A LYS* 3.5 12.7 - - - +
852A SER* 3.0 42.0 + - - +
855A ALA* 4.0 5.7 - - - +
856A ALA* 4.0 6.1 - - - +
861A HIS* 4.5 8.9 + - - -
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Residues in contact with GLY 569 (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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565A SER 3.0 11.3 + - - -
566A THR 3.3 0.9 + - - -
568A ARG* 1.3 73.2 - - - +
570A CYS* 1.3 65.2 + - - +
572A ALA* 3.2 7.0 + - - +
573A ILE* 3.0 25.8 + - - +
721A LEU* 4.8 1.1 - - - -
848A ALA* 3.3 30.5 - - - -
851A LEU* 4.2 5.7 - - - +
852A SER* 3.9 8.5 - - - -
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Residues in contact with CYS 570 (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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541A ALA* 4.4 18.2 - - - -
542A GLY* 4.5 5.6 - - - -
543A PRO 3.7 21.0 - - - +
544A LEU* 4.1 28.5 - - - -
545A CYS 5.4 0.3 + - - -
553A VAL* 5.6 0.4 - - - -
566A THR* 2.9 23.6 + - - -
567A ASN* 3.4 11.9 - - - +
568A ARG 3.2 0.2 - - - -
569A GLY* 1.3 76.1 - - - +
571A ARG* 1.3 56.0 + - - +
573A ILE* 3.2 7.3 + - - +
574A GLY* 2.8 28.1 + - - -
845A THR* 5.4 3.6 - - - -
848A ALA* 3.6 15.6 - - - +
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Residues in contact with ARG 571 (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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100A COA 2.9 38.7 + - + +
543A PRO* 6.6 0.2 - - - -
567A ASN 3.1 13.1 + - - +
568A ARG 3.3 10.1 - - - +
570A CYS* 1.3 76.8 - - - +
572A ALA* 1.3 62.3 + - - +
574A GLY* 3.4 1.7 + - - +
575A LEU* 3.1 59.4 + - + +
720A VAL* 4.1 16.8 - - + +
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Residues in contact with ALA 572 (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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568A ARG 3.1 9.0 + - - +
569A GLY 3.2 7.4 + - - +
571A ARG* 1.3 75.4 - - - +
573A ILE* 1.3 65.3 + - - +
575A LEU 3.6 0.2 + - - -
576A GLY* 3.2 16.3 + - - -
712A ILE* 3.7 13.6 - - + +
716A VAL* 3.6 28.7 - - + +
720A VAL* 4.2 3.8 - - + +
721A LEU* 4.0 31.6 - - + -
851A LEU* 4.4 5.4 - - + -
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Residues in contact with ILE 573 (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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544A LEU* 4.5 8.5 - - + -
545A CYS 4.0 13.2 - - - +
569A GLY 3.0 12.4 + - - +
570A CYS* 3.5 7.9 - - - +
572A ALA* 1.3 76.6 - - - +
574A GLY* 1.3 61.3 + - - +
576A GLY* 3.1 8.0 + - - -
577A GLY 3.5 0.2 + - - -
578A GLY* 3.0 25.4 + - - +
579A ALA* 3.8 30.3 - - + +
710A ALA* 4.6 2.5 - - + -
712A ILE* 3.9 10.3 - - + +
844A GLY 4.3 4.0 - - - +
847A MET* 3.6 26.9 - - + -
848A ALA* 3.8 33.7 - - + +
851A LEU* 3.7 16.4 - - + -
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Residues in contact with GLY 574 (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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543A PRO 5.5 0.4 - - - -
545A CYS* 4.0 28.1 - - - +
570A CYS 2.8 15.4 + - - -
571A ARG* 3.8 2.0 - - - -
573A ILE* 1.3 78.6 - - - +
575A LEU* 1.3 61.0 + - - +
576A GLY 3.2 0.9 + - - -
577A GLY* 3.2 12.6 + - - -
578A GLY 3.9 0.7 + - - -
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Residues in contact with LEU 575 (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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571A ARG* 3.1 54.3 + - - +
572A ALA 3.6 0.2 + - - -
573A ILE 3.4 0.2 - - - -
574A GLY* 1.3 74.8 - - - +
576A GLY* 1.3 56.3 + - - +
577A GLY 3.3 2.0 + - - -
713A PRO* 4.1 5.0 - - - +
716A VAL* 3.8 28.2 - - + +
720A VAL* 3.7 29.8 - - + -
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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