Contacts of the strand formed by residues 625 - 635 (chain A) in PDB entry 2RC4
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 GLY 625 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542A PHE* 4.6 0.9 - - - -
563A PHE* 3.8 13.0 - - - -
621A ASN* 3.3 2.5 - - - -
622A ASP* 2.9 33.8 + - - -
623A VAL 3.0 2.6 + - - -
624A LYS* 1.3 80.3 - - - +
626A CYS* 1.3 65.6 + - - -
627A HIS* 3.3 13.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 626 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542A PHE* 3.7 12.9 - - - -
563A PHE 3.1 7.6 + - - -
564A HIS* 3.7 33.2 - - + -
565A PRO* 4.0 1.2 - - - +
569A GLU* 5.5 4.0 - - - -
579A PHE* 4.2 11.2 - - + -
619A THR* 3.6 18.6 - - - +
621A ASN* 3.0 35.9 - - - +
625A GLY* 1.3 72.0 - - - -
627A HIS* 1.3 61.3 + - - +
628A LEU 3.8 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 627 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541A GLU* 2.3 35.8 + - + +
542A PHE* 3.9 7.9 - + - -
619A THR* 3.0 4.5 - - - -
620A GLN* 2.9 54.3 + - + +
622A ASP* 2.9 36.9 + - - -
624A LYS* 3.8 15.7 - - + +
625A GLY* 3.3 26.2 + - - -
626A CYS* 1.3 69.6 - - - +
628A LEU* 1.3 66.7 + - - +
629A VAL* 3.2 1.0 + - - +
653A TYR* 4.2 16.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 628 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A PHE* 4.0 23.5 - - + -
541A GLU* 4.3 11.9 + - - +
544A LEU* 3.9 25.1 - - + -
565A PRO* 6.0 1.1 - - + -
589A TYR* 3.9 22.0 - - - +
593A LEU* 4.2 14.6 - - + -
596A LEU* 4.5 5.8 - - + -
617A VAL* 5.0 7.4 - - + -
618A LEU 3.9 6.5 - - - +
619A THR* 4.0 6.3 - - + +
626A CYS 3.8 3.6 + - - -
627A HIS* 1.3 70.7 - - - +
629A VAL* 1.3 59.2 + - - +
630A GLY* 3.7 20.4 - - - +
648A MET* 5.2 2.7 - - + -
650A LEU* 3.6 28.0 - - + -
653A TYR* 3.5 16.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 629 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618A LEU* 2.9 37.9 + - + +
619A THR* 3.4 11.9 - - - -
620A GLN* 3.5 13.7 - - + +
627A HIS 4.2 0.4 - - - +
628A LEU* 1.3 77.9 - - - +
630A GLY* 1.3 56.7 + - - +
649A ILE* 3.7 4.2 - - + +
650A LEU* 3.2 21.4 + - - -
653A TYR* 3.5 45.4 - - + -
658A TYR* 3.9 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 630 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617A VAL* 3.5 2.1 - - - +
618A LEU* 2.6 37.2 + - - +
628A LEU* 3.6 15.1 - - - +
629A VAL* 1.3 81.0 - - - +
631A TYR* 1.3 56.7 + - - +
648A MET* 3.3 17.0 - - - -
649A ILE* 4.1 5.6 - - - -
650A LEU 4.4 1.6 - - - -
662A LEU* 4.2 5.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 631 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593A LEU* 3.7 31.9 - - + -
594A CYS* 5.1 0.9 - - - -
597A ALA* 3.3 34.9 - - + +
601A LEU* 4.4 0.3 - - - +
604A LYS* 3.3 19.8 + - - -
615A PHE* 4.0 12.5 - + + -
616A TYR 3.1 14.6 - - - +
617A VAL* 3.7 17.7 - - + -
628A LEU* 5.9 0.2 - - + -
630A GLY* 1.3 76.1 - - - +
632A PHE* 1.3 83.0 + - - +
633A SER* 3.4 22.4 - - - -
646A CYS* 4.0 11.6 - - + -
648A MET* 2.9 55.0 + - + +
662A LEU* 3.2 12.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 632 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614A LEU 4.0 0.3 - - - +
615A PHE* 3.9 0.7 - - - -
616A TYR* 3.0 65.9 + + + +
631A TYR* 1.3 86.3 - - - +
633A SER* 1.3 70.6 + - - +
634A LYS* 4.5 4.5 - - + -
643A ASN 4.2 9.4 - - - -
644A VAL* 4.2 9.2 - - + -
646A CYS 3.0 15.9 - - - +
647A ILE* 3.8 14.1 - - + -
662A LEU* 3.7 42.6 - - + -
665A PHE* 4.0 13.9 - + - -
666A SER* 3.5 27.4 - - - -
669A LEU* 4.1 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 633 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604A LYS* 4.0 7.8 + - - -
613A PHE* 4.3 8.5 - - - -
614A LEU 3.9 4.0 + - - -
615A PHE* 3.5 20.8 - - - +
631A TYR* 3.4 17.2 - - - -
632A PHE* 1.3 80.7 - - - +
634A LYS* 1.3 60.7 + - - +
644A VAL* 3.6 0.7 - - - -
645A SER* 2.7 32.4 + - - -
646A CYS* 2.7 32.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 634 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613A PHE* 3.4 4.5 - - - -
614A LEU* 2.8 41.5 + - + +
616A TYR* 4.1 25.0 + - + +
632A PHE* 4.5 3.6 - - + -
633A SER* 1.3 77.7 - - - +
635A GLU* 1.3 71.0 + - - +
636A LYS 3.4 0.3 + - - -
642A TYR 4.4 3.6 - - - +
643A ASN* 3.3 35.4 - - - +
645A SER* 3.9 4.9 - - - +
666A SER 5.8 0.2 - - - +
669A LEU* 3.6 30.8 - - + +
673A GLU* 3.7 32.3 + - - -
776A TRP* 4.6 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 635 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612A PRO* 3.7 7.0 - - + +
613A PHE* 3.4 35.3 - - + -
634A LYS* 1.3 80.0 - - - +
636A LYS* 1.3 69.2 + - - +
637A HIS 4.2 12.9 - - - +
638A CYS* 4.4 9.4 + - + +
639A GLN* 4.1 26.1 + - - +
642A TYR* 5.0 16.1 + - + +
645A SER* 4.1 8.3 + - - +
680A GLU* 3.8 17.7 - - - +
----------------------------------------------------------
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