Contacts of the strand formed by residues 654 - 662 (chain A) in PDB entry 5MJ6
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 ILE 654 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610A TRP* 4.2 6.3 - - + -
617A PRO* 3.7 20.2 - - + -
619A VAL* 4.1 9.4 - - + -
632A GLN* 3.6 38.8 - - + +
652A TRP* 3.7 15.7 - - + +
653A HIS* 1.3 75.5 - - - +
655A PRO* 1.3 64.7 - - + +
656A LEU* 3.0 19.4 + - + +
673A LEU* 3.4 5.2 - - - +
674A LEU* 3.0 42.2 + - + +
700A TYR* 3.5 37.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 655 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558A MET* 3.8 35.4 - - + -
562A TYR* 3.9 33.4 - - + -
606A MET* 3.7 23.8 - - + -
610A TRP* 4.8 0.2 - - - +
653A HIS 3.6 9.4 - - - +
654A ILE* 1.3 82.6 - - + +
656A LEU* 1.3 61.2 + - - +
657A SER* 3.3 5.1 + - - -
671A VAL* 4.6 0.7 - - - -
672A SER 3.7 6.1 - - - +
673A LEU* 4.6 4.7 - - + -
698A GLY* 5.3 3.1 - - - -
700A TYR* 3.5 14.6 + - - -
1138A BR 4.5 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 656 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619A VAL* 4.0 21.8 - - + -
630A ILE* 3.6 36.6 - - + -
654A ILE* 3.0 26.4 + - + +
655A PRO* 1.3 69.8 - - - +
657A SER* 1.3 63.1 + - - +
658A TYR* 4.0 4.4 - - + -
671A VAL* 3.4 3.0 - - - -
672A SER* 2.8 40.0 + - - +
674A LEU* 4.0 19.1 - - + +
681A ILE* 4.4 16.6 - - + -
692A VAL* 4.5 7.9 - - + -
700A TYR* 3.7 19.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 657 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
655A PRO 3.3 5.8 + - - -
656A LEU* 1.3 75.5 - - - +
658A TYR* 1.3 65.9 + - - +
670A SER 3.5 9.0 - - - -
671A VAL* 4.3 4.3 - - - -
692A VAL* 3.5 5.9 - - - +
693A ASN* 2.9 22.8 + - - -
694A ILE* 2.8 47.1 + - - +
697A ASN* 5.8 1.9 - - - +
700A TYR* 3.9 2.6 + - - -
1138A BR 3.9 23.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 658 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628A LEU* 4.8 3.6 - - + -
656A LEU* 4.0 6.3 - - + -
657A SER* 1.3 80.5 - - - +
659A VAL* 1.3 65.3 + - - +
660A THR* 5.0 1.8 - - - -
668A TYR* 3.1 32.9 + + - -
669A GLN* 3.2 4.5 - - - +
670A SER* 3.1 58.4 + - - -
671A VAL* 4.5 0.4 - - - -
672A SER* 4.2 10.1 + - - -
681A ILE* 3.4 40.4 - - + +
682A ASN 4.1 4.5 + - - -
683A LEU* 3.7 28.9 - - + -
690A VAL* 4.5 9.6 - - + -
691A LYS 3.4 12.6 - - - +
692A VAL* 4.3 13.5 - - + -
694A ILE* 3.4 5.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 659 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658A TYR* 1.3 74.6 - - - +
660A THR* 1.3 70.3 + - - +
667A LYS* 5.0 15.7 - - + -
668A TYR 3.4 12.3 - - - +
669A GLN* 3.6 23.3 - - + +
689A TRP* 3.6 19.9 - - + -
690A VAL* 3.7 2.1 - - - +
691A LYS* 3.1 39.6 + - + +
694A ILE* 3.9 14.5 - - + +
722A VAL 5.8 1.3 - - - +
723A LEU* 4.2 13.5 - - + -
727A ASP* 4.8 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 660 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658A TYR* 5.0 2.9 - - + -
659A VAL* 1.3 79.7 - - - +
661A GLU* 1.3 64.0 + - - +
662A GLY 5.1 0.4 - - - +
667A LYS* 3.3 9.2 - - - +
668A TYR* 2.9 68.0 + - + +
683A LEU* 4.8 6.8 - - + +
685A GLU* 4.9 2.2 - - - +
687A VAL* 3.2 28.4 - - + +
689A TRP* 3.0 26.7 + - - -
690A VAL* 3.8 10.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 661 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
660A THR* 1.3 77.6 + - - +
662A GLY* 1.3 64.5 + - - +
665A TYR* 3.7 36.2 - - - +
666A SER 3.5 10.8 - - - +
667A LYS* 3.9 22.0 - - + -
687A VAL* 3.3 5.3 - - - +
688A LEU* 2.8 45.0 + - + +
689A TRP* 3.5 37.8 + - + +
715A GLN* 4.3 6.8 + - - +
722A VAL* 4.1 11.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 662 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
660A THR* 4.2 0.8 - - - +
661A GLU* 1.3 77.1 - - - +
663A ARG* 1.3 67.0 + - - -
664A ASN* 3.2 5.4 - - - -
665A TYR* 3.2 10.0 + - - -
666A SER 3.1 13.8 + - - -
685A GLU* 3.5 23.3 + - - -
686A GLU 3.4 14.4 - - - -
687A VAL* 4.1 0.9 - - - -
688A LEU* 3.7 12.8 - - - +
----------------------------------------------------------
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