Contacts of the strand formed by residues 570 - 579 (chain D) in PDB entry 3P23
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 SER 570 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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564D VAL 3.7 5.8 + - - -
565D ILE* 3.7 13.8 - - - +
566D VAL* 3.3 13.1 - - - +
567D GLY* 3.9 1.3 - - - +
568D LYS 3.0 12.8 - - - -
569D ILE* 1.3 79.2 + - - +
571D PHE* 1.3 66.0 + - - +
589D GLY* 3.9 0.5 - - - -
590D MET* 2.8 50.5 + - - +
591D PHE 5.0 1.1 + - - -
598D VAL* 4.0 1.2 - - - +
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Residues in contact with PHE 571 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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563D VAL* 3.8 2.6 - - - +
564D VAL* 2.7 62.1 + - + +
566D VAL* 5.8 1.3 - - + -
569D ILE* 5.7 1.6 - - + -
570D SER* 1.3 79.7 - - - +
572D CYS* 1.3 68.1 + - - +
573D PRO* 3.7 20.0 - - + -
587D TYR* 3.4 44.9 - + + -
589D GLY* 3.8 12.1 - - - +
590D MET 4.5 0.2 - - - +
598D VAL* 3.6 34.5 - - + -
600D ARG* 5.5 4.0 - - - -
639D TYR* 3.4 30.3 - + - -
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Residues in contact with CYS 572 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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562D SER* 3.3 22.0 - - - -
563D VAL* 3.9 15.3 - - + +
571D PHE* 1.3 83.1 - - - +
573D PRO* 1.3 89.8 - - - +
574D LYS* 5.1 1.3 - - - -
575D ASP* 3.3 26.2 + - - +
587D TYR* 4.2 4.2 - - - +
588D ARG 3.9 10.2 + - - +
589D GLY* 4.6 0.6 - - - -
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Residues in contact with PRO 573 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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561D THR 4.1 14.1 - - - +
562D SER 3.7 17.3 - - - +
563D VAL* 3.8 0.7 - - - -
564D VAL* 3.6 35.2 - - + +
571D PHE* 3.7 14.8 - - + +
572D CYS* 1.3 101.3 - - - +
574D LYS* 1.3 91.6 + - + +
575D ASP* 3.0 4.0 - - - +
587D TYR* 4.4 9.4 - - + -
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Residues in contact with LYS 574 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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604C GLU* 4.2 17.3 + - - +
572D CYS* 5.1 1.5 - - - -
573D PRO* 1.3 90.0 - - + +
575D ASP* 1.3 59.3 + - - +
576D VAL* 3.9 11.6 - - - +
587D TYR* 5.0 1.4 - - - -
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Residues in contact with ASP 575 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572D CYS* 3.3 26.3 - - - +
573D PRO 2.9 3.7 + - - +
574D LYS* 1.3 79.3 - - - +
576D VAL* 1.3 65.4 - - - +
577D LEU* 3.4 3.1 + - - -
587D TYR* 3.9 4.8 - - - -
588D ARG* 2.8 66.9 + - - +
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Residues in contact with VAL 576 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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604C GLU* 6.1 1.6 - - + -
574D LYS* 3.9 8.0 - - - +
575D ASP* 1.3 78.6 - - - +
577D LEU* 1.3 66.4 + - - +
578D GLY 3.5 28.3 - - - +
579D HIS* 4.5 8.3 - - + -
585D ILE* 3.6 30.7 - - + -
586D VAL 4.1 2.7 - - - +
587D TYR* 3.8 13.9 - - + -
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Residues in contact with LEU 577 (chain D).
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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575D ASP 3.4 2.4 + - - -
576D VAL* 1.3 76.9 - - - +
578D GLY* 1.3 59.0 + - - +
586D VAL* 2.9 21.5 + - + +
587D TYR 4.0 12.8 - - - +
588D ARG* 3.3 51.6 - - + +
597D ALA* 4.1 9.9 - - + -
644D LEU* 3.6 28.5 - - + -
645D CYS 5.6 0.9 - - - +
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Residues in contact with GLY 578 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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576D VAL* 3.5 13.8 - - - +
577D LEU* 1.3 82.4 - - - +
579D HIS* 1.3 61.1 + - - -
580D GLY 4.1 0.2 - - - -
585D ILE* 3.9 0.9 - - - +
586D VAL* 3.2 32.1 + - - +
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Residues in contact with HIS 579 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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582C GLU* 4.5 7.6 + - - -
604C GLU* 3.9 26.5 + - + +
605C CYS* 3.7 29.8 - - - -
717C LYS 6.1 0.7 - - - -
576D VAL* 4.5 7.4 - - + -
578D GLY* 1.3 72.5 - - - -
580D GLY* 1.3 68.0 + - - +
583D GLY 4.1 12.5 - - - -
584D THR 3.9 7.1 + - - -
585D ILE* 4.0 21.9 - - + +
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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