Contacts of the strand formed by residues 649 - 655 (chain A) in PDB entry 5HG1
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 LEU 649 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529A LEU* 4.3 20.4 - - + -
582A ILE* 5.2 1.1 - - + -
586A LEU* 5.7 0.7 - - + -
594A VAL 5.7 1.1 - - - +
596A LEU 3.5 11.7 - - - +
598A LEU* 4.8 14.6 - - + -
638A LYS* 5.6 5.0 - - - +
641A ILE* 4.1 24.9 - - + +
647A PHE* 3.3 35.2 + - + -
648A ASP* 1.3 76.9 - - - +
650A ASP* 1.3 60.9 + - - +
651A VAL* 3.8 6.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 650 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596A LEU 3.3 8.2 + - - +
597A PRO* 3.4 12.3 - - + +
598A LEU* 2.9 23.3 + - - -
638A LYS* 5.6 2.6 + - - +
649A LEU* 1.3 69.6 - - - +
651A VAL* 1.3 67.0 + - - +
652A VAL* 3.2 11.8 + - - +
912A ARG* 2.8 35.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 651 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598A LEU* 3.7 25.4 - - + +
600A PHE* 5.2 0.4 - - + -
612A ASP* 3.9 12.5 - - - +
634A VAL* 3.3 35.7 - - + -
637A LEU* 3.9 26.2 - - + -
638A LYS* 4.1 30.9 + - + +
641A ILE* 4.7 10.5 - - + -
649A LEU 3.8 5.9 + - - +
650A ASP* 1.3 75.0 + - - +
652A VAL* 1.3 61.0 + - - +
653A ALA 4.4 10.1 - - - +
654A VAL* 5.0 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 652 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597A PRO* 4.1 5.8 - - + -
598A LEU 3.0 5.6 + - - +
611A LEU* 3.8 9.9 - - + +
612A ASP* 3.4 18.0 - - - +
650A ASP* 3.5 31.0 - - - +
651A VAL* 1.3 74.5 - - - +
653A ALA* 1.3 60.8 + - + +
905A THR* 3.9 32.1 - - + +
908A ALA* 3.7 30.3 - - + -
909A CYS* 4.6 2.0 - - - -
912A ARG* 4.1 22.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 653 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598A LEU 3.7 3.4 + - - +
599A GLY* 3.8 2.6 - - - -
600A PHE* 3.0 30.7 + - - +
611A LEU* 3.4 31.6 - - + -
612A ASP* 4.4 1.6 - - - +
651A VAL* 3.7 4.5 - - - +
652A VAL* 1.3 82.0 - - + +
654A VAL* 1.3 64.6 + - - +
655A VAL* 4.6 4.3 - - + -
901A ALA* 5.3 1.3 - - - +
904A ILE* 4.3 13.7 - - + -
905A THR* 4.2 13.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 654 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A THR 5.1 0.2 - - - +
600A PHE* 3.1 40.4 - - + +
602A PHE* 5.0 7.0 - - + -
608A GLN* 2.6 45.7 + - - +
611A LEU* 3.0 10.1 + - - +
613A GLU 4.5 0.4 - - - +
614A SER* 3.2 31.2 - - - +
633A VAL* 5.1 1.8 - - + -
634A VAL* 3.4 25.4 - - + -
651A VAL* 5.0 0.7 - - + -
653A ALA* 1.3 73.7 - - - +
655A VAL* 1.3 66.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 655 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A THR* 5.6 1.6 - - - +
516A VAL* 4.2 12.6 - - + -
600A PHE 2.8 14.5 + - - +
601A THR* 3.2 15.3 - - - +
602A PHE* 2.9 27.2 + - - -
608A GLN* 5.0 2.0 - - - +
611A LEU* 4.6 0.9 - - + -
653A ALA* 4.6 5.2 - - + -
654A VAL* 1.3 83.0 - - - +
656A ASN* 1.3 69.6 + - - +
659A VAL* 4.1 9.4 - - + -
660A GLY* 4.2 9.2 - - - +
901A ALA* 4.2 16.2 - - + -
904A ILE* 3.7 33.2 - - + -
----------------------------------------------------------
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