Contacts of the strand formed by residues 563 - 569 (chain A) in PDB entry 6IRT
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 ARG 563 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536A SER* 4.3 1.1 - - - -
555A ILE* 5.2 0.9 - - + -
556A ARG 3.9 5.4 - - - +
557A HIS* 3.6 24.6 + - + +
558A TRP 2.4 27.8 + - - +
559A ASP* 2.6 27.6 + - - +
560A GLN* 3.6 1.8 - - - +
561A ASN 3.1 24.2 + - - -
562A GLU* 1.3 77.4 - - - +
564A PHE* 1.3 60.7 + - - +
587A SER* 3.5 40.2 + - - +
588A ALA* 5.8 2.2 - - - -
626A ARG* 3.5 8.8 - - - +
627A PHE* 3.2 62.4 + - + +
629A TYR* 3.6 33.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 564 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530A GLN* 4.4 3.6 - - + -
534A GLU* 3.6 44.9 - - + -
536A SER* 3.9 11.2 - - - -
537A LEU* 3.9 29.2 - - + -
555A ILE* 3.3 27.2 - - - +
556A ARG* 3.2 16.7 + - + +
562A GLU* 3.3 33.4 - - + -
563A ARG* 1.3 73.3 - - - +
565A LEU* 1.3 63.5 + - - +
566A VAL* 5.5 2.7 - - + -
597A LEU* 4.3 15.3 - - + -
624A LEU* 3.9 16.6 - - + -
625A LEU 3.6 16.6 - - - -
626A ARG* 3.8 21.1 - - + +
627A PHE* 3.8 4.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 565 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545A PHE* 4.0 7.6 - - + -
553A SER* 4.0 17.0 - - - +
554A TYR 3.3 18.8 - - - +
555A ILE* 3.7 17.3 - - + -
564A PHE* 1.3 78.6 - - - +
566A VAL* 1.3 63.4 + - - +
567A VAL* 4.2 9.1 + - + -
579A LEU* 4.5 11.7 - - + -
590A LEU* 4.5 11.2 - - + -
594A ALA* 5.8 0.4 - - + -
612A LEU* 4.3 16.2 - - + -
623A LEU 3.7 0.7 - - - +
624A LEU* 3.8 1.7 - - - -
625A LEU* 3.0 60.9 + - + +
627A PHE* 4.1 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 566 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456A LEU* 4.0 10.3 - - + -
460A THR* 3.8 20.4 - - + -
552A PHE 3.8 1.1 - - - +
553A SER* 3.3 5.7 + - - -
554A TYR* 3.1 61.9 + - + +
556A ARG* 6.2 1.3 - - + -
564A PHE* 5.5 2.5 - - + -
565A LEU* 1.3 78.4 - - - +
567A VAL* 1.3 65.9 + - - +
568A LEU* 3.7 25.4 - - + -
623A LEU 3.3 10.1 - - - +
624A LEU* 3.7 21.1 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
551A LEU* 4.0 27.6 - - + -
552A PHE 3.9 2.2 - - - -
553A SER* 4.0 16.6 - - - +
565A LEU* 4.2 12.3 - - + -
566A VAL* 1.3 78.4 - - - +
568A LEU* 1.3 64.8 + - - +
577A ALA* 5.9 1.1 - - - -
579A LEU* 4.3 22.7 - - + -
615A LEU* 5.1 8.1 - - + -
617A LEU* 4.1 20.3 - - + +
621A GLU 4.3 0.7 - - - +
622A GLY* 3.3 2.6 - - - -
623A LEU* 2.8 47.0 + - + +
625A LEU* 5.3 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 568 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453A LEU* 3.7 29.2 - - + +
456A LEU* 4.3 10.1 - - + -
457A MET* 4.0 27.1 - - + +
550A GLY 3.4 0.2 - - - +
551A LEU* 3.3 31.2 - - - +
552A PHE* 3.2 47.5 + - + +
554A TYR* 4.0 9.6 - - + +
566A VAL* 3.7 19.7 - - + -
567A VAL* 1.3 81.9 - - - +
569A ASN* 1.3 60.3 + - - +
570A PHE* 3.9 9.4 + - + -
617A LEU* 5.9 0.2 - - - -
621A GLU 4.4 0.2 - - - -
622A GLY* 4.2 6.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 569 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453A LEU* 3.3 11.7 - - - +
550A GLY 3.5 8.7 - - - +
551A LEU* 4.4 6.5 - - + -
568A LEU* 1.3 73.8 - - - +
570A PHE* 1.3 60.9 + - - +
571A GLY* 2.9 31.1 + - - +
573A VAL 3.7 11.3 + - - +
575A LEU* 4.3 8.1 - - - +
617A LEU* 4.2 13.7 - - + +
618A GLU 2.3 35.6 + - - -
619A PRO* 3.5 1.0 - - - +
620A HIS* 3.3 22.1 - - - +
621A GLU 3.3 24.0 + - - +
----------------------------------------------------------
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