Contacts of the strand formed by residues 689 - 696 (chain A) in PDB entry 5I4E
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 ASN 689 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A ALA* 6.0 0.2 - - - +
184A SER* 5.1 6.9 + - - -
188A ASP* 5.4 4.4 + - - -
190A GLU* 5.4 3.8 - - + +
191A ASP 3.0 9.3 + - - +
192A GLN* 3.5 36.4 + - - +
193A SER 3.2 17.5 + - - +
688A THR* 1.4 70.3 - - - +
690A PRO* 1.3 74.8 + - - +
691A SER* 5.3 0.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 690 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A SER* 3.3 19.3 - - - +
195A LEU* 3.9 12.3 - - + -
505A LEU* 6.0 2.5 - - + -
509A THR* 3.8 33.0 - - + +
685A LEU* 5.4 2.7 - - + +
688A THR* 3.4 12.3 - - - +
689A ASN* 1.3 98.2 + - - +
691A SER* 1.3 59.8 + - - +
692A PHE* 3.9 19.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 691 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A LEU 5.5 5.4 + - - -
177A VAL* 3.1 27.3 + - - +
181A ALA* 4.9 10.3 - - - -
193A SER 2.8 12.1 + - - -
194A ILE* 3.4 16.4 - - - +
195A LEU* 2.8 26.5 + - - +
689A ASN 5.3 0.4 - - - -
690A PRO* 1.3 74.0 - - - +
692A PHE* 1.3 62.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 692 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A LEU 5.4 0.4 + - - -
141A PHE* 3.7 16.1 - - + +
142A CYS* 3.3 23.4 + - - +
177A VAL* 5.4 0.3 - - - +
195A LEU* 3.4 40.8 - - + -
197A THR* 4.3 10.1 - - + -
502A LEU* 4.5 9.0 - - + -
505A LEU* 4.1 10.3 - - + -
506A PHE* 3.7 48.5 - + + -
509A THR* 4.1 17.7 - - + -
510A MET* 5.2 6.1 - - + -
690A PRO* 3.9 24.2 - - + -
691A SER* 1.3 76.8 + - - +
693A VAL* 1.3 66.2 + - - +
694A ARG* 3.8 15.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 693 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A TYR* 5.3 2.9 - - + -
142A CYS* 3.6 12.8 - - + +
144A VAL* 3.5 29.6 - - + -
174A VAL* 5.3 8.7 - - + -
177A VAL* 4.0 30.5 - - + -
194A ILE* 4.4 15.3 - - + -
195A LEU 2.8 10.1 + - - -
196A CYS* 3.3 17.3 - - - -
197A THR 2.8 26.5 + - - -
207A ASN* 4.8 6.5 - - - +
692A PHE* 1.3 78.4 - - - +
694A ARG* 1.3 59.8 + - - +
695A CYS* 3.3 9.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 694 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A PHE* 3.6 21.5 - - + -
142A CYS 2.9 17.3 + - - +
143A VAL* 3.6 10.8 - - + -
144A VAL 3.1 23.1 + - - +
197A THR* 2.7 47.3 + - - +
503A GLN* 2.7 28.1 + - - -
506A PHE* 3.2 28.9 - - - +
692A PHE* 3.8 24.2 - - - -
693A VAL* 1.3 69.5 - - - +
695A CYS* 1.4 62.5 + - - +
696A ILE* 3.7 5.9 + - + +
719A ASN* 2.9 46.7 + - - +
721A VAL* 4.6 6.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 695 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A VAL* 3.5 24.7 - - + -
196A CYS* 4.3 4.5 - - - -
197A THR 2.8 21.0 + - - +
198A GLY* 3.5 12.8 - - - -
202A ALA* 3.4 34.2 - - + +
203A GLY 3.7 6.1 - - - +
204A LYS* 3.6 27.1 - - + +
207A ASN* 3.8 5.2 - - - -
693A VAL* 4.1 11.9 - - - -
694A ARG* 1.4 70.4 - - - +
696A ILE* 1.4 64.9 + - - +
715A GLN* 4.2 2.4 - - - +
719A ASN* 4.7 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 696 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A LEU* 6.0 0.4 - - + -
143A VAL* 3.9 16.2 - - + -
144A VAL 2.8 14.5 + - - +
145A ILE* 3.5 13.6 - - + -
146A ASN 3.1 24.3 + - - -
202A ALA* 3.8 5.1 - - - +
694A ARG* 3.8 13.5 - - + +
695A CYS* 1.4 78.5 - - - +
697A VAL* 1.3 72.1 + - - +
698A PRO 3.7 0.3 - - - -
712A VAL* 3.9 26.7 - - + -
715A GLN* 3.3 31.0 - - + +
716A LEU* 4.5 12.3 - - + -
719A ASN* 3.5 28.5 - - - +
721A VAL* 5.4 0.9 - - + -
----------------------------------------------------------
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