Contacts of the strand formed by residues 565 - 571 (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 LYS 565 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493A GLY 5.0 0.2 + - - -
494A LYS 4.1 9.3 + - - +
495A VAL* 3.4 29.1 - - + +
496A ASP* 2.9 39.3 + - - +
497A ALA 3.1 9.0 + - - -
563A GLY 3.8 2.2 + - - +
564A SER* 1.3 68.6 - - - +
566A ILE* 1.3 59.5 + - - +
567A VAL* 4.9 0.9 - - + -
592A SER* 3.2 38.1 - - - +
594A GLU* 3.9 14.1 - - + +
649A GLU* 2.9 26.2 + - - -
650A LEU* 3.7 27.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 566 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497A ALA* 3.4 16.6 - - + +
499A VAL* 3.7 31.2 - - + +
552A PHE* 6.6 0.4 - - + -
555A LEU* 3.7 28.5 - - + -
560A PHE* 4.4 3.8 - - + -
564A SER* 3.4 29.6 + - - +
565A LYS* 1.3 78.6 - - - +
567A VAL* 1.3 63.2 + - - +
568A VAL* 3.6 4.8 + - + +
591A TYR* 3.7 32.8 - - + -
592A SER 3.1 20.8 + - - +
593A LEU* 3.6 3.9 - - + -
594A GLU* 3.4 11.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 567 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495A VAL* 3.7 19.3 - - + -
497A ALA 3.0 5.5 + - - -
498A PHE* 3.5 23.2 - - + +
499A VAL* 2.9 30.2 + - - +
565A LYS* 4.9 1.8 - - + -
566A ILE* 1.3 71.6 - - - +
568A VAL* 1.3 60.1 + - - +
569A HIS* 3.2 37.5 + - + +
594A GLU* 3.9 15.9 - - + -
596A LEU* 3.8 11.9 - - + -
658A GLN* 3.2 26.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 568 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499A VAL* 3.6 13.9 - - + -
501A ILE* 4.2 25.8 - - + -
552A PHE* 5.5 6.1 - - + -
566A ILE* 3.6 14.8 + - + +
567A VAL* 1.3 70.5 - - - +
569A HIS* 1.3 60.0 + - - +
570A ARG* 3.2 13.2 + - + +
582A PHE* 4.4 11.2 - - + -
593A LEU* 4.0 20.2 - - + -
594A GLU 2.8 36.5 + - - +
595A LEU* 3.9 16.2 - - + -
596A LEU 3.0 15.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 569 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498A PHE* 4.2 4.8 - + - -
499A VAL 3.0 9.2 + - - +
500A GLY* 3.4 2.9 - - - -
501A ILE 3.2 22.1 + - - +
567A VAL* 3.4 19.8 + - + +
568A VAL* 1.3 71.4 - - - +
570A ARG* 1.3 60.7 + - - +
596A LEU* 3.2 36.8 - - + +
598A ILE* 3.7 20.6 - - + -
655A LEU 4.4 1.0 + - - -
658A GLN* 4.4 4.3 - - + -
659A ILE* 3.2 24.5 - - + +
662A LEU* 3.5 24.6 - - + +
676A PRO* 6.0 0.4 - - + -
678A THR* 3.4 34.2 + - - +
679A VAL* 3.7 5.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 570 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501A ILE* 3.4 22.4 - - - +
502A ASP* 3.2 21.2 + - - +
503A ILE* 3.0 36.3 + - - +
568A VAL* 3.2 11.7 + - + +
569A HIS* 1.3 70.8 - - - +
571A ASP* 1.3 84.4 + - - +
572A GLY 3.1 12.0 + - - +
573A ARG 3.4 16.7 + - - -
574A LEU* 3.5 32.3 - - + +
575A TYR* 4.3 6.5 - - - -
578A GLU* 2.9 31.9 + - - -
582A PHE* 4.8 2.5 - - - -
596A LEU 3.0 11.6 + - - +
597A GLU 3.8 0.2 - - - -
598A ILE* 2.9 29.6 + - - +
679A VAL* 4.2 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 571 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501A ILE 3.2 7.3 + - - -
502A ASP* 3.5 21.7 - - + +
569A HIS 3.8 1.2 + - - -
570A ARG* 1.3 93.8 + - - +
572A GLY* 1.3 58.2 + - - +
573A ARG 4.1 0.2 + - - -
598A ILE 4.1 4.2 - - - +
600A LYS* 3.4 19.2 - - - +
679A VAL* 3.6 32.3 - - + +
683A ASP* 2.8 43.5 - - - +
11M G 5.2 0.2 + - - -
12M G 4.0 11.6 + - - +
----------------------------------------------------------
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