Contacts of the helix formed by residues 618 - 638 (chain A) in PDB entry 4GFG
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 618 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486A GLU* 3.6 11.7 - - - -
552A LYS* 3.9 15.0 - - - +
555A VAL* 3.9 7.9 - - - -
617A PRO* 1.3 73.8 - - - +
619A PHE* 1.3 66.1 + - - -
620A ALA* 3.2 3.1 - - - -
621A ALA* 3.1 10.1 + - - +
622A VAL* 3.1 20.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 619 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479A SER* 4.5 6.3 - - - -
482A MET* 3.6 47.1 - - + -
483A LYS* 3.7 21.8 - - + +
486A GLU* 2.9 23.7 + - + +
495A LEU* 4.5 0.4 - - + -
551A SER* 3.6 13.5 - - - -
554A ASP* 3.6 17.5 - - + -
555A VAL* 3.5 38.6 - - + -
558A PHE* 3.8 28.5 - + + -
618A GLY* 1.3 68.5 - - - -
620A ALA* 1.3 56.6 + - - +
622A VAL* 3.6 13.9 - - + -
623A GLU* 2.6 37.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 620 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A LYS* 4.0 27.9 + - + +
486A GLU* 3.6 12.0 + - - +
618A GLY 3.2 1.1 - - - -
619A PHE* 1.3 78.5 - - - +
621A ALA* 1.3 62.3 + - - +
623A GLU* 4.0 2.4 - - - +
624A LEU* 3.1 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 621 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617A PRO* 4.2 17.3 - - + -
618A GLY 3.1 11.9 + - - +
620A ALA* 1.3 79.5 - - - +
622A VAL* 1.3 58.5 + - - +
624A LEU* 3.5 6.6 + - - +
625A ARG* 3.1 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 622 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479A SER* 4.6 3.1 - - - -
555A VAL* 4.2 15.7 - - + -
558A PHE* 3.7 35.4 - - + -
604A LEU* 4.3 17.9 - - + -
608A CYS* 4.5 5.4 - - - -
617A PRO* 4.2 21.8 - - + -
618A GLY 3.1 19.8 + - - +
619A PHE* 3.9 10.8 - - + +
621A ALA* 1.3 74.8 - - - +
623A GLU* 1.3 64.1 + - - +
625A ARG* 3.5 6.4 + - - +
626A LEU* 3.1 27.1 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
476A HIS* 2.7 27.5 + - - -
479A SER* 3.6 28.7 - - - +
480A MET* 3.8 27.8 - - + +
483A LYS* 3.7 22.8 + - + -
619A PHE 2.6 23.0 + - - +
620A ALA 4.0 0.6 - - - +
622A VAL* 1.3 74.5 - - - +
624A LEU* 1.3 56.6 + - - +
626A LEU 3.3 0.5 + - - -
627A ARG* 2.8 62.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 624 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620A ALA 3.1 17.9 + - - +
621A ALA* 3.9 7.2 - - - +
623A GLU* 1.3 77.5 + - - +
625A ARG* 1.3 66.3 + - - +
627A ARG* 3.4 33.2 - - - +
628A ASN* 3.0 52.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 625 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600A GLU* 3.5 43.1 + - - +
601A MET* 4.9 2.9 - - + +
604A LEU* 4.1 27.8 - - + +
607A LEU* 6.4 0.9 - - + -
621A ALA 3.1 17.7 + - - +
622A VAL* 3.7 8.5 - - - +
624A LEU* 1.3 78.2 - - - +
626A LEU* 1.3 58.9 + - - +
628A ASN* 4.6 9.8 - - - +
629A TYR* 3.3 32.6 + - - +
632A ASP* 5.6 2.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 626 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472A ILE* 4.4 8.4 - - + +
475A VAL* 3.9 18.6 - - + +
476A HIS* 3.8 20.1 - - + +
479A SER* 3.7 13.2 - - - +
558A PHE* 3.7 37.0 - - + -
562A MET* 4.8 2.2 - - + -
601A MET* 3.6 30.7 - - + -
604A LEU* 3.7 16.6 - - + -
622A VAL 3.1 16.3 + - - +
623A GLU 3.8 3.1 - - - +
625A ARG* 1.3 74.7 - - - +
627A ARG* 1.3 66.4 + - - +
629A TYR* 3.8 2.9 - - - +
630A TYR* 3.0 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 627 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476A HIS* 3.4 19.5 - - + +
483A LYS* 4.1 12.1 - - - +
623A GLU* 2.8 46.2 + - - +
624A LEU* 3.4 32.0 - - - +
626A LEU* 1.3 78.7 - - - +
628A ASN* 1.3 66.4 + - - +
630A TYR* 3.3 2.9 + - - +
631A TYR* 3.2 61.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 628 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624A LEU* 3.0 46.7 + - - +
625A ARG* 4.2 12.3 - - - +
627A ARG* 1.3 81.6 - - - +
629A TYR* 1.3 62.8 + - - +
631A TYR* 3.2 11.2 + - - +
632A ASP* 3.0 31.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 629 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472A ILE* 3.8 17.5 - - + -
598A PRO* 3.3 17.1 - - + +
600A GLU* 3.2 44.0 + - + -
601A MET* 3.7 39.9 - - + -
625A ARG* 3.3 30.6 + - - +
626A LEU 4.0 3.1 - - - +
627A ARG 3.4 0.2 - - - -
628A ASN* 1.3 78.6 - - - +
630A TYR* 1.3 61.9 + - - +
632A ASP* 3.5 15.2 + - + -
633A VAL* 3.1 46.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 630 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469A LYS* 3.6 40.8 - - + +
472A ILE* 3.8 26.2 - - + +
473A GLU* 3.7 36.9 + - + -
476A HIS* 5.0 13.7 - + + +
626A LEU 3.0 17.9 + - - +
627A ARG* 3.7 5.6 - - - +
628A ASN 3.2 0.2 - - - -
629A TYR* 1.3 76.5 - - - +
631A TYR* 1.3 79.8 + + - +
633A VAL* 3.2 4.8 + - + +
634A VAL* 2.9 50.4 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
476A HIS* 4.9 5.9 - + - -
627A ARG* 3.2 49.1 + - + +
628A ASN* 3.2 11.2 + - - +
630A TYR* 1.3 100.0 - + - +
632A ASP* 1.3 62.2 + - - +
633A VAL 3.1 0.2 - - - -
634A VAL* 3.7 10.0 - - + +
635A ASN* 2.8 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 632 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625A ARG* 5.6 1.7 + - - -
628A ASN* 3.0 19.4 + - - +
629A TYR* 3.6 23.8 - - + +
631A TYR* 1.3 77.0 - - - +
633A VAL* 1.3 58.4 + - + +
635A ASN* 3.5 7.8 + - - +
636A GLU* 3.1 35.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 633 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A ASP* 5.8 1.1 - - - +
469A LYS* 3.6 37.0 - - + +
472A ILE* 4.1 9.6 - - + -
629A TYR* 3.1 47.5 + - + +
630A TYR* 3.5 9.4 - - + +
631A TYR 3.1 0.2 - - - -
632A ASP* 1.3 76.2 - - + +
634A VAL* 1.3 58.8 - - - +
636A GLU* 3.5 9.9 + - + +
637A GLY* 3.0 24.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 634 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469A LYS* 4.1 17.9 - - - +
630A TYR* 2.9 62.6 + - + +
631A TYR* 3.2 12.1 + - + +
633A VAL* 1.3 75.4 - - - +
635A ASN* 1.3 62.5 - - - +
637A GLY* 3.5 1.4 + - - -
638A HIS* 2.9 48.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 635 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631A TYR 2.8 17.1 + - - +
632A ASP* 3.5 9.4 + - - +
634A VAL* 1.3 75.4 - - - +
636A GLU* 1.3 70.1 + - - +
638A HIS* 3.1 21.3 + - - +
639A HIS* 3.3 29.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 636 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632A ASP* 3.1 21.0 + - + +
633A VAL* 3.5 10.9 + - + +
634A VAL 3.5 0.2 - - - -
635A ASN* 1.3 84.6 - - - +
637A GLY* 1.3 62.3 + - - +
639A HIS* 3.0 30.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 637 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469A LYS* 5.9 5.8 - - - -
633A VAL 3.0 17.2 + - - -
634A VAL* 3.5 3.3 + - - -
635A ASN 3.2 0.4 - - - -
636A GLU* 1.3 73.1 - - - +
638A HIS* 1.3 58.4 + - - +
639A HIS 2.9 18.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 638 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634A VAL* 2.9 40.8 + - + +
635A ASN* 3.1 14.4 + - - +
637A GLY* 1.3 76.0 - - - +
639A HIS* 1.3 66.2 + - + +
----------------------------------------------------------
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