Contacts of the strand formed by residues 618 - 623 (chain A) in PDB entry 6A5N
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 618 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518A PRO 4.4 2.6 - - - +
519A ILE* 3.4 37.0 - - + +
520A SER 4.0 1.2 + - - -
614A ILE* 3.9 20.9 - - + -
616A LEU* 3.2 17.1 + - + +
617A PRO* 1.3 82.4 - - - +
619A GLU* 1.3 62.5 + - - +
630A VAL* 4.6 11.2 - - + -
631A ARG 3.5 11.9 - - - +
632A CYS* 3.8 17.0 - - + -
633A LEU* 6.0 1.7 - - - +
636A ILE* 5.3 1.3 - - + -
642A ILE* 4.2 24.2 - - + +
643A CYS* 4.4 2.2 - - + -
712A VAL* 4.4 20.0 - - + -
755A LEU* 4.2 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 619 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502A ARG* 5.0 10.6 + - - -
519A ILE* 3.9 3.1 - - - -
520A SER* 3.2 21.4 - - - +
522A VAL* 3.2 21.4 - - - +
618A LEU* 1.3 76.0 - - - +
620A ILE* 1.3 69.1 + - - +
630A VAL* 3.5 4.2 - - - +
631A ARG* 2.7 83.5 + - + +
632A CYS* 5.1 0.2 - - - +
633A LEU* 4.4 25.3 - - + +
752A LEU* 5.8 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 620 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510A ILE* 3.4 32.1 - - + -
519A ILE* 4.4 6.1 - - + -
520A SER 2.9 7.9 + - - +
521A ALA* 3.2 18.7 - - + -
522A VAL* 2.9 25.3 + - - +
530A PRO* 3.8 7.9 - - + -
619A GLU* 1.3 75.7 - - - +
621A PHE* 1.3 62.8 + - - +
628A TRP* 3.7 22.4 - - + -
629A GLY 3.1 13.2 - - - +
630A VAL* 4.1 3.8 - - + -
712A VAL* 3.9 20.2 - - + -
715A PHE* 3.8 35.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 621 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522A VAL* 3.1 24.0 - - + +
619A GLU* 4.5 0.2 - - - +
620A ILE* 1.3 76.0 - - - +
622A LYS* 1.3 79.0 + - - +
623A THR* 3.2 23.8 - - + -
628A TRP* 3.5 8.1 - - - -
629A GLY 2.9 49.8 + - - -
630A VAL 3.7 2.7 - - - -
631A ARG* 3.3 61.7 - - + +
752A LEU 5.2 1.6 - - - -
754A GLU* 3.5 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 622 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522A VAL 3.1 8.9 + - - -
523A ASN* 3.5 41.0 - - + +
524A GLU* 6.0 0.5 - - - +
525A ILE* 4.3 23.5 + - + +
526A ASP* 3.7 19.8 + - - +
528A GLU* 3.4 23.1 + - - +
621A PHE* 1.3 83.6 - - - +
623A THR* 1.3 75.2 + - - +
624A LYS 5.9 0.4 + - - -
627A GLY* 3.9 10.1 - - - +
628A TRP* 3.4 34.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 623 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525A ILE* 5.3 2.2 - - - -
621A PHE* 3.2 38.8 - - + +
622A LYS* 1.3 83.0 + - - +
624A LYS* 1.3 67.3 + - - +
625A SER* 4.4 0.4 - - - -
626A ARG* 2.9 34.1 + - + -
627A GLY 2.7 28.3 + - - +
628A TRP 4.7 0.2 - - - -
629A GLY 4.2 4.0 - - - +
754A GLU* 3.9 16.2 - - - +
----------------------------------------------------------
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