Contacts of the strand formed by residues 610 - 618 (chain A) in PDB entry 3DPK
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 VAL 610 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600A THR* 3.8 23.3 - - + -
601A ALA 3.4 2.0 - - - +
602A PHE* 3.9 31.4 - - + -
603A GLY 4.4 2.2 - - - +
609A ALA* 1.3 76.3 - - - +
611A LEU* 1.3 64.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 611 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600A THR* 3.4 5.0 - - - -
601A ALA* 2.8 36.4 + - + +
604A LEU* 4.7 14.8 - - + -
609A ALA* 4.6 10.1 - - + +
610A VAL* 1.3 78.3 - - - +
612A LYS* 1.3 86.3 + - + +
613A VAL* 3.6 17.1 + - + +
650A LEU* 4.2 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 612 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586A LYS* 5.9 0.4 - - - +
598A GLU* 2.8 28.5 + - - +
599A ALA 3.3 8.7 - - - +
600A THR* 4.5 8.3 - - + +
611A LEU* 1.3 94.9 - - + +
613A VAL* 1.3 58.4 + - - +
664A GLU* 5.6 0.2 - - - -
665A TYR* 3.7 38.2 + - + +
667A CYS* 5.7 2.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 613 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582A LEU* 4.2 1.3 - - + -
598A GLU* 3.5 6.9 - - - +
599A ALA* 2.7 53.3 + - + +
601A ALA* 4.0 13.9 - - + -
604A LEU* 3.9 15.0 - - + -
611A LEU* 3.8 19.1 - - + +
612A LYS* 1.3 78.8 - - - +
614A ALA* 1.3 60.0 + - - +
615A VAL* 4.1 5.2 - - + -
650A LEU* 3.8 20.9 - - + -
662A ILE* 3.9 17.3 - - + -
663A THR 3.6 7.2 - - - +
665A TYR* 3.6 11.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 614 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588A LEU* 4.4 4.5 - - + -
596A VAL* 3.9 9.4 - - + -
597A VAL 3.5 5.4 - - - +
598A GLU* 4.6 0.9 - - - +
613A VAL* 1.3 73.3 - - - +
615A VAL* 1.3 61.6 + - - +
616A LYS 4.2 0.4 - - - -
661A VAL 3.6 0.3 - - - +
662A ILE* 3.4 4.2 - - - +
663A THR* 2.8 45.0 + - - +
664A GLU 4.0 0.9 - - - +
665A TYR* 3.9 2.8 - - + +
923A 8C5 3.5 40.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 615 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582A LEU* 4.4 10.8 - - + -
584A PHE* 4.0 11.4 - - + -
596A VAL* 3.2 4.9 - - - -
597A VAL* 2.8 46.4 + - + +
599A ALA* 3.7 28.3 - - + -
613A VAL* 4.1 9.6 - - + -
614A ALA* 1.3 78.6 - - - +
616A LYS* 1.3 62.4 + - - +
617A MET* 3.8 17.3 - - + +
660A LEU* 3.9 27.4 - - + -
661A VAL 3.3 8.7 - - - +
662A ILE* 4.6 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 616 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594A GLY* 5.8 0.7 - - - -
595A LYS 3.5 7.4 - - - +
596A VAL* 3.7 16.4 - - + -
614A ALA 4.2 0.2 - - - -
615A VAL* 1.3 73.6 - - - +
617A MET* 1.3 67.5 + - - +
630A LEU* 3.8 21.8 - - + +
633A GLU* 2.5 36.5 + - - +
659A VAL 3.9 0.7 - - - +
660A LEU* 3.4 6.8 - - - -
661A VAL* 2.8 46.3 + - + +
663A THR* 5.9 0.6 + - - +
796A ASP 3.0 9.7 + - - -
797A PHE* 4.5 1.2 - - - +
799A LEU* 4.6 10.6 - - + +
800A ALA* 4.2 10.8 - - + +
923A 8C5 2.7 43.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 617 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584A PHE* 3.9 22.4 - - + -
594A GLY* 3.5 3.3 - - - -
595A LYS* 2.9 65.2 + - + +
597A VAL* 3.8 25.1 - - + -
615A VAL* 3.8 27.4 - - + +
616A LYS* 1.3 76.7 - - - +
618A LEU* 1.3 73.3 + - - +
630A LEU* 4.5 5.6 - - - -
658A PRO* 5.8 3.1 - - + -
659A VAL 3.8 7.4 - - - +
660A LEU* 3.6 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 618 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593A PHE* 3.5 16.2 - - + +
594A GLY* 5.2 1.3 - - - -
595A LYS* 4.5 4.5 - - - -
617A MET* 1.3 89.9 - - - +
619A LYS* 1.3 68.5 + - - +
622A ALA* 3.9 14.8 - - + -
626A GLU* 3.5 23.3 - - + +
627A LYS* 3.0 48.0 - - + +
630A LEU* 4.0 22.9 - - + +
658A PRO* 6.0 3.7 - - + +
659A VAL* 4.4 7.7 + - + +
799A LEU* 5.5 5.2 - - + -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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