Contacts of the helix formed by residues 620 - 631 (chain A) in PDB entry 3EA4
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 620 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615A VAL* 3.8 14.1 - - + -
616A THR 5.4 0.3 + - - -
617A LYS* 3.0 35.2 + - - +
619A ALA* 1.3 78.8 - - - +
621A LEU* 1.3 62.4 + - - +
622A ARG 3.6 0.7 - - - -
623A GLU* 3.6 11.2 + - - +
624A ALA* 3.1 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 621 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462A ILE* 3.8 26.9 - - + -
466A TYR* 3.8 22.4 - - + -
467A ALA* 3.7 25.6 - - + -
470A VAL* 4.7 3.8 - - + -
615A VAL* 3.9 28.3 - - + -
617A LYS 3.6 3.4 + - - +
618A LYS* 3.1 17.5 + - - +
619A ALA 3.2 0.4 - - - -
620A ASP* 1.3 75.5 - - - +
622A ARG* 1.3 65.9 + - - +
624A ALA* 3.1 2.6 + - - +
625A ILE* 3.0 47.5 + - + +
639A VAL* 4.3 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 622 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466A TYR* 4.2 17.2 + - - -
470A VAL* 4.1 28.9 - - + +
473A GLU* 2.6 42.2 + - - +
474A LEU* 3.6 22.4 - - + +
618A LYS 4.6 1.4 + - - -
619A ALA 4.6 4.8 + - - +
620A ASP 3.6 0.4 - - - -
621A LEU* 1.3 76.8 - - - +
623A GLU* 1.3 58.3 + - - +
626A GLN* 3.1 27.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 623 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619A ALA 5.3 1.7 + - - +
620A ASP* 3.6 12.2 + - - +
621A LEU 3.2 0.6 - - - -
622A ARG* 1.3 77.2 - - - +
624A ALA* 1.3 60.9 + - - +
626A GLN* 3.3 7.3 + - + +
627A THR* 2.8 39.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 624 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613A ALA* 6.1 1.3 - - + -
614A ARG 5.5 0.7 - - - +
615A VAL* 3.8 16.6 - - + -
620A ASP 3.1 16.9 + - - +
621A LEU* 3.1 6.6 + - - +
623A GLU* 1.3 76.6 - - - +
625A ILE* 1.3 56.9 + - - +
627A THR* 3.3 7.9 + - - -
628A MET* 3.0 26.2 + - - +
635A TYR* 5.0 2.3 + - - -
637A LEU* 3.8 31.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 625 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467A ALA 3.7 23.8 - - - +
470A VAL* 3.9 15.0 - - + -
471A LEU* 3.9 30.1 - - + +
474A LEU* 3.9 17.0 - - + -
561A LEU* 4.1 13.7 - - + -
621A LEU* 3.0 34.5 + - + +
624A ALA* 1.3 73.0 - - - +
626A GLN* 1.3 64.8 + - - +
628A MET* 3.3 8.0 + - + +
629A LEU* 3.0 27.3 + - + +
637A LEU* 3.6 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 626 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474A LEU* 3.3 35.0 + - + +
622A ARG* 3.1 20.2 + - + +
623A GLU* 3.6 10.5 - - + +
625A ILE* 1.3 76.0 - - - +
627A THR* 1.3 57.5 + - - +
629A LEU* 3.3 8.8 + - - +
630A ASP* 2.9 73.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 627 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623A GLU* 2.8 24.8 + - - +
624A ALA* 3.4 11.2 - - - -
626A GLN* 1.3 74.5 - - - +
628A MET* 1.3 56.5 + - - +
630A ASP* 4.0 4.0 - - - +
631A THR* 2.6 48.6 + - - +
635A TYR* 3.7 20.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 628 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471A LEU* 3.9 28.7 - - + -
533A VAL* 4.5 4.3 - - + -
559A LYS* 3.0 48.0 + - + +
560A VAL 3.9 17.7 - - - +
561A LEU* 4.3 12.3 - - + -
624A ALA 3.0 13.5 + - - +
625A ILE* 3.4 20.0 - - + +
627A THR* 1.3 77.7 - - - +
629A LEU* 1.3 61.5 + - + +
630A ASP 3.5 0.2 + - - -
631A THR 3.8 3.5 - - - +
635A TYR* 3.6 38.9 - - + +
637A LEU* 3.9 21.5 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
471A LEU* 4.5 8.1 - - + -
474A LEU* 3.8 35.0 - - + +
475A THR* 3.8 29.2 - - + -
531A ILE* 3.8 22.2 - - + -
533A VAL* 4.7 0.7 - - + -
559A LYS* 3.7 20.9 + - + +
625A ILE* 3.0 30.3 + - + +
626A GLN* 3.8 11.0 - - - +
627A THR 3.3 0.2 - - - -
628A MET* 1.3 84.0 - - + +
630A ASP* 1.3 66.5 + - - +
631A THR 4.6 0.2 - - - -
632A PRO* 5.7 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 630 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626A GLN* 2.9 51.5 + - - +
627A THR* 4.0 4.4 - - - +
629A LEU* 1.3 79.8 - - - +
631A THR* 1.3 65.5 + - - +
632A PRO* 3.1 11.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 631 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559A LYS* 2.7 26.7 + - - -
611A PRO* 4.5 14.8 - - + -
627A THR* 2.6 30.6 + - - +
628A MET 4.3 0.2 - - - -
629A LEU 3.6 0.2 - - - -
630A ASP* 1.3 74.3 - - - +
632A PRO* 1.3 80.2 - - + +
633A GLY 3.5 1.2 - - - +
634A PRO 5.2 0.8 - - - +
635A TYR* 3.6 30.5 - - + -
----------------------------------------------------------
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