Contacts of the helix formed by residues 625 - 640 (chain A) in PDB entry 4PJW
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 ASP 625 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582A ALA* 4.7 12.4 - - + +
623A HIS* 3.7 4.6 + - - +
624A THR* 1.3 78.8 + - - +
626A THR* 1.3 65.9 + - - +
627A ASP* 3.0 33.5 + - - +
628A VAL* 3.2 27.9 + - + +
629A LEU* 3.3 24.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 626 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624A THR 3.5 2.5 + - - -
625A ASP* 1.3 76.6 + - - +
627A ASP* 1.3 67.7 + - - +
629A LEU* 3.5 7.4 + - - +
630A GLU* 3.1 33.0 + - + +
692A LYS* 4.1 22.8 + - - +
732A HIS* 4.2 11.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 627 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586A THR* 4.1 21.4 - - + +
625A ASP* 3.0 13.6 + - - +
626A THR* 1.3 82.5 - - - +
628A VAL* 1.3 66.5 + - - +
630A GLU* 3.2 15.0 + - - +
631A ALA* 2.9 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 628 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582A ALA* 3.6 28.7 - - + +
585A VAL* 3.8 11.7 - - + -
586A THR* 3.6 19.1 - - - +
589A LEU* 4.0 0.3 - - - +
619A ILE* 3.6 30.7 - - + -
623A HIS* 3.8 19.5 - - + +
625A ASP* 3.2 25.3 + - + +
627A ASP* 1.3 76.6 - - - +
629A LEU* 1.3 59.5 + - + +
631A ALA* 3.2 6.4 + - - +
632A CYS* 3.0 27.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 629 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620A VAL* 3.6 31.4 - - + +
623A HIS* 3.6 30.3 - - + +
624A THR* 4.0 8.5 - - - +
625A ASP 3.3 16.9 + - - +
626A THR* 3.9 5.4 - - - +
627A ASP 3.2 0.2 - - - -
628A VAL* 1.3 75.7 - - + +
630A GLU* 1.3 66.4 + - - +
632A CYS* 3.3 4.6 + - - +
633A SER* 3.0 25.8 + - - -
692A LYS* 3.9 29.8 - - + +
693A ARG* 4.0 19.1 - - + +
696A ALA* 4.0 16.1 - - + +
697A PHE* 4.9 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 630 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626A THR* 3.1 20.3 + - + +
627A ASP* 3.2 19.9 + - - +
629A LEU* 1.3 75.9 - - - +
631A ALA* 1.3 58.2 + - - +
633A SER* 3.8 5.0 - - - -
634A LYS* 2.9 62.1 + - + +
696A ALA* 4.5 6.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 631 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586A THR* 4.2 16.6 - - + +
589A LEU* 3.7 25.6 - - + -
590A GLN* 4.2 13.7 - - - +
593A GLN* 4.8 1.5 + - - +
627A ASP 2.9 13.2 + - - +
628A VAL 3.4 9.0 - - - +
629A LEU 3.2 0.2 - - - -
630A GLU* 1.3 78.3 - - - +
632A CYS* 1.3 54.1 + - - +
634A LYS* 3.8 6.1 - - - +
635A THR* 2.6 39.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 632 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
589A LEU* 3.8 11.9 - - - +
616A ILE* 4.2 15.8 - - + +
619A ILE* 3.7 25.8 - - - -
620A VAL* 3.6 35.9 - - + -
628A VAL* 3.0 19.2 + - - +
629A LEU* 3.6 9.4 - - - +
631A ALA* 1.3 76.7 - - - +
633A SER* 1.3 57.3 + - - +
635A THR* 3.3 5.7 + - - -
636A TYR* 2.9 33.6 + - - +
697A PHE* 4.3 4.3 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
629A LEU 3.0 17.5 + - - -
630A GLU* 3.8 4.0 - - - -
632A CYS* 1.3 75.8 - - - +
634A LYS* 1.3 63.0 + - - +
636A TYR 3.3 0.7 + - - -
637A HIS* 3.1 10.9 + - - +
696A ALA* 2.9 32.3 + - - -
697A PHE* 3.4 25.1 - - - -
700A ALA* 3.2 17.8 - - - +
701A HIS* 3.1 20.8 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
590A GLN* 5.9 2.2 - - - +
593A GLN* 3.8 22.3 + - - +
630A GLU* 2.9 56.7 + - + +
631A ALA* 3.9 4.3 - - - +
633A SER* 1.3 74.8 - - - +
635A THR* 1.3 61.2 + - - +
637A HIS* 3.5 9.4 + - - +
638A ALA* 3.3 18.0 + - - +
700A ALA* 5.0 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 635 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
589A LEU* 2.7 29.5 + - + +
592A PRO* 3.9 31.4 - - + -
593A GLN* 4.2 6.8 + - + +
616A ILE* 4.0 22.4 - - + -
631A ALA 2.6 25.4 + - - -
632A CYS* 3.5 6.3 - - - -
634A LYS* 1.3 73.8 - - - +
636A TYR* 1.3 66.8 + - - +
637A HIS 3.0 1.8 - - - -
638A ALA* 2.9 16.7 + - - +
639A LEU* 3.1 15.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 636 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613A LEU* 3.5 29.8 + - + +
616A ILE* 3.5 36.8 - - + -
617A ARG* 3.5 13.4 + - + +
632A CYS 2.9 13.1 + - - +
633A SER 3.3 0.2 + - - -
635A THR* 1.3 76.4 - - - +
637A HIS* 1.3 57.2 + - - +
639A LEU* 3.7 5.8 + - - +
640A CYS* 3.1 33.5 + - - +
650A VAL* 3.8 28.3 - - + -
653A SER* 3.7 16.1 + - - -
654A ARG* 3.9 30.5 - - + -
657A LEU* 4.2 14.8 - - + -
697A PHE* 3.8 17.3 - + + -
701A HIS* 3.6 18.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 637 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633A SER 3.1 12.5 + - - +
634A LYS* 3.5 12.4 + - - +
635A THR 3.0 0.4 - - - -
636A TYR* 1.3 76.2 - - - +
638A ALA* 1.3 67.5 + - - +
640A CYS* 3.2 21.3 + - - +
641A ASN* 3.9 1.7 + - - +
654A ARG* 5.3 3.6 - - - -
700A ALA* 3.4 31.9 + - + -
701A HIS* 3.3 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 638 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592A PRO* 4.7 6.1 - - + +
593A GLN* 4.2 31.0 - - + +
597A LEU* 3.6 18.8 - - + +
634A LYS 3.3 10.0 + - - +
635A THR* 2.9 9.9 + - - +
637A HIS* 1.3 83.6 + - - +
639A LEU* 1.3 62.3 + - + +
640A CYS 3.5 0.2 + - - -
641A ASN* 3.7 10.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 639 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592A PRO* 4.4 15.9 - - + +
597A LEU* 3.8 30.6 - - + +
600A TYR* 4.3 16.8 - - + -
609A LEU* 4.4 8.1 - - + -
612A LEU* 3.9 18.8 - - + -
613A LEU* 3.7 27.4 - - + -
616A ILE* 4.4 3.8 - - + -
635A THR* 3.1 28.3 + - + +
636A TYR* 4.1 3.6 - - - +
638A ALA* 1.3 76.0 - - - +
640A CYS* 1.3 56.1 + - - +
641A ASN* 3.1 11.5 + - - +
644A PHE* 6.0 0.5 - - - +
646A ILE* 4.5 8.9 - - + +
647A PHE* 4.6 2.8 + - - -
650A VAL* 3.7 30.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 640 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636A TYR* 3.1 24.9 + - - +
637A HIS* 3.2 14.8 + - + +
639A LEU* 1.3 74.0 - - - +
641A ASN* 1.3 59.2 + - - +
642A GLU 3.7 0.9 + - - -
647A PHE* 3.7 19.5 - - + +
650A VAL* 3.5 27.6 - - - -
651A ASP* 4.2 9.6 - - - -
654A ARG* 3.5 48.0 + - - +
----------------------------------------------------------
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