Contacts of the strand formed by residues 608 - 615 (chain B) in PDB entry 2R5N
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 608 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625A LEU* 4.0 20.9 - - - +
553B ILE* 3.2 20.4 - - + +
555B ILE* 4.4 10.8 - - + -
601B LEU* 3.2 39.1 + - - +
602B PRO 2.9 27.9 + - - -
603B LYS* 3.9 8.7 + - - +
605B VAL 2.7 20.6 + - - +
606B THR* 2.9 12.9 + - - +
607B ALA* 1.3 78.5 - - - +
609B VAL* 1.3 61.8 + - - +
622B TYR* 2.8 29.1 + - - +
623B VAL* 3.7 21.3 - - + +
627B GLY* 3.2 4.3 - - - -
628B ALA 2.9 24.8 + - - +
662B LEU* 3.6 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 609 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552B LEU* 4.0 18.8 - - + -
553B ILE 2.8 8.5 + - - +
554B PHE* 3.2 27.9 - - + +
555B ILE* 2.8 25.2 + - - +
608B ARG* 1.3 76.4 - - - +
610B ALA* 1.3 70.0 + - - +
611B VAL* 3.9 6.9 + - + -
623B VAL* 4.5 1.3 - - - -
628B ALA* 3.3 14.8 - - + +
630B VAL* 4.3 15.5 - - + -
655B VAL* 4.8 4.5 - - + +
658B LYS* 5.0 1.3 - - + -
659B ALA* 4.0 15.5 - - + -
662B LEU* 3.7 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 610 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555B ILE* 3.2 11.7 - - + +
609B VAL* 1.3 73.7 - - - +
611B VAL* 1.3 59.0 + - - +
612B GLU 4.3 0.4 - - - -
619B TRP* 3.6 46.0 - - + -
623B VAL* 3.8 14.3 - - + +
628B ALA 3.0 9.8 + - - +
629B ILE* 3.6 4.2 - - + -
630B VAL 2.8 30.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 611 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554B PHE* 4.3 7.0 - - + -
555B ILE 2.8 11.4 + - - +
556B ALA* 3.4 25.8 - - + -
557B THR 3.6 1.4 + - - -
560B GLU* 3.5 23.1 - - + +
563B LEU* 3.9 29.6 - - + -
564B ALA* 4.5 8.1 - - + +
609B VAL* 4.0 21.3 - - + +
610B ALA* 1.3 80.3 - - - +
612B GLU* 1.3 65.0 + - - +
619B TRP* 5.8 0.6 - - - -
630B VAL* 3.4 18.6 - - + +
650B PHE* 4.5 0.7 - - + -
655B VAL* 4.2 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 612 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479B VAL* 4.8 5.5 - - - +
483B ARG* 2.7 42.0 + - - -
492B ARG* 3.7 14.1 - - - +
557B THR* 2.5 27.9 + - - +
560B GLU* 3.7 7.2 - - - -
610B ALA 4.3 0.2 - - - -
611B VAL* 1.3 77.2 - - - +
613B ALA* 1.3 62.2 + - - +
614B GLY* 2.8 25.7 + - - +
615B ILE 4.9 1.2 + - - +
618B TYR* 5.5 0.3 - - - +
619B TRP* 2.9 31.6 + - + +
629B ILE* 6.1 0.2 - - - +
630B VAL 3.1 5.7 + - - -
631B GLY* 3.2 21.5 - - - -
650B PHE* 3.6 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 613 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462B ASP 4.7 1.9 - - - +
463B SER* 3.7 26.8 - - - -
464B ILE* 4.2 7.1 + - + +
475B PRO 4.3 7.3 - - - +
492B ARG* 4.5 2.9 + - - -
560B GLU* 2.8 30.8 + - - +
612B GLU* 1.3 70.4 - - - +
614B GLY* 1.3 55.5 + - - +
632B MET* 4.0 7.3 - - + +
645B PHE* 4.0 17.0 - - + -
650B PHE* 3.4 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 614 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476B VAL* 3.2 16.2 - - - -
479B VAL* 6.5 1.1 - - - -
612B GLU* 2.8 24.5 + - - +
613B ALA* 1.3 74.0 - - - +
615B ILE* 1.3 68.9 + - - -
616B ALA* 3.3 0.5 + - - -
619B TRP* 5.4 1.0 - - - -
631B GLY* 3.6 1.6 - - - -
632B MET* 2.8 24.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 615 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484A VAL* 3.3 38.4 - - + +
486A PRO* 4.1 9.0 - - + -
476B VAL* 2.7 29.4 + - + +
477B GLU* 4.0 12.3 - - - -
480B ALA* 3.7 29.8 - - + -
612B GLU* 4.9 1.4 + - - +
614B GLY* 1.3 70.9 - - - +
616B ALA* 1.3 65.8 + - - +
617B ASP 4.3 5.4 - - - +
618B TYR* 3.6 16.5 + - - +
619B TRP* 4.0 6.8 + - - -
632B MET 3.4 13.2 - - - +
633B THR* 4.2 2.2 - - - -
673B EDO 3.5 28.3 - - - +
----------------------------------------------------------
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