Contacts of the strand formed by residues 161 - 167 (chain I) in PDB entry 6RAR
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 LYS 161 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159I ILE 4.9 0.3 - - - +
160I GLY* 1.3 71.4 - - - -
162I LYS* 1.3 65.5 + - - +
294I ASN* 5.1 6.3 - - + +
295I VAL 3.3 8.3 - - - +
296I ASP* 2.7 44.6 + - + +
325I ASP* 4.9 0.3 - - - +
326I PRO* 3.0 29.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 162 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157I LYS* 3.2 29.4 + - - +
158I MET* 4.4 3.4 - - - +
159I ILE 3.6 12.6 + - - +
160I GLY 3.9 3.1 - - - +
161I LYS* 1.3 82.4 - - - +
163I GLN* 1.3 59.0 + - - +
164I ILE* 3.9 7.5 + - + -
294I ASN* 3.2 8.2 - - - +
295I VAL* 2.8 36.1 + - + +
297I LEU* 3.6 22.7 - - + -
323I ILE* 3.7 30.2 + - + -
324I LYS 3.4 13.7 - - - +
325I ASP* 4.5 17.2 - - - +
326I PRO* 4.0 0.7 - - - -
336I HIS 4.7 6.9 + - - -
339I LEU* 4.5 11.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 163 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162I LYS* 1.3 71.0 - - - +
164I ILE* 1.3 62.4 + - - +
165I GLU* 2.8 25.8 + - - +
266I GLN* 3.9 15.9 - - - +
267I THR* 3.9 27.5 + - - +
270I SER* 2.9 25.5 + - - -
292I TRP* 3.6 34.8 + - + -
293I GLU 3.8 3.4 - - - -
294I ASN* 4.0 12.2 - - - +
322I MET 3.6 1.7 - - - +
324I LYS* 2.7 49.7 + - + +
326I PRO* 4.1 5.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 164 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162I LYS* 4.1 7.4 - - + +
163I GLN* 1.3 74.1 - - - +
165I GLU* 1.3 68.0 + - - +
166I ILE* 6.4 0.2 - - + -
292I TRP* 3.2 7.3 - - - -
293I GLU* 2.8 37.8 + - - +
295I VAL* 3.8 22.4 - - + -
297I LEU* 5.9 0.4 - - + -
306I PHE* 3.8 21.3 - - + -
309I LEU* 4.0 27.8 - - + -
321I VAL* 4.1 22.7 - - + -
322I MET 3.3 5.6 - - - +
323I ILE* 3.6 36.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 165 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300D AMP 3.3 20.3 + - - +
163I GLN* 2.8 31.6 + - + +
164I ILE* 1.3 82.8 - - - +
166I ILE* 1.3 67.3 + - - +
249I PHE* 3.9 5.5 - - - +
266I GLN* 4.8 0.5 + - - -
270I SER* 4.2 3.5 + - - -
290I LEU* 3.4 14.0 - - + +
291I GLU 3.4 19.7 - - - +
292I TRP* 3.5 10.4 - - + +
321I VAL* 3.2 8.4 - - - +
322I MET* 2.7 39.0 + - + -
324I LYS* 3.3 24.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 166 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300D AMP 3.0 25.7 + - - -
164I ILE* 6.4 0.2 - - + -
165I GLU* 1.3 75.7 - - - +
167I LYS* 1.3 66.7 + - - +
168I LEU* 3.8 11.6 + - + +
290I LEU* 3.9 9.6 - - + +
291I GLU 4.8 3.1 + - - +
309I LEU 5.3 1.6 - - - +
313I ALA* 3.7 29.2 - - + +
318I TYR* 3.3 51.4 - - + -
320I GLY 3.9 2.0 - - - -
321I VAL* 4.7 2.7 - - + -
322I MET 4.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 167 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C MN 3.6 2.0 + - - -
32D C 3.3 17.2 - - - -
300D AMP 3.2 57.4 + - + -
165I GLU 3.6 1.0 + - - -
166I ILE* 1.3 74.8 - - - +
168I LEU* 1.3 58.7 - - - +
318I TYR* 3.9 0.2 - - - +
319I GLU* 2.8 60.6 + - + +
320I GLY 3.1 24.4 + - - +
321I VAL 3.9 9.9 - - - +
322I MET* 3.9 17.9 - - + -
340I LYS* 4.1 10.5 - - + -
342I LYS* 4.2 20.7 - - + +
----------------------------------------------------------
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