Contacts of the strand formed by residues 180 - 186 (chain A) in PDB entry 3RKR
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 ARG 180 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A ARG* 5.9 1.6 - - - +
136A GLY 2.9 16.3 + - - +
137A HIS* 3.3 42.5 + - - +
138A ILE 2.8 30.9 + - - +
178A GLN 4.6 4.8 + - - -
179A VAL* 1.3 77.8 - - - +
181A VAL* 1.3 57.0 + - - +
182A SER* 4.0 2.2 + - - -
222A GLN* 3.8 17.8 + - - +
223A ALA 3.1 19.2 + - - -
224A ASP* 3.4 22.0 + - - +
226A SER 2.8 37.2 + - - -
227A PHE* 3.7 33.2 - - + +
237D LEU* 3.7 21.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 181 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A LEU* 4.8 0.4 - - + -
138A ILE* 3.1 17.5 - - + +
140A ASN* 3.6 22.9 - - - +
167A MET* 3.6 32.5 - - + +
170A ALA* 4.1 2.5 - - + -
171A ALA* 3.9 31.0 - - + +
174A LEU* 3.7 33.2 - - + -
179A VAL 4.1 0.4 + - - -
180A ARG* 1.3 73.7 - - - +
182A SER* 1.3 63.3 + - - +
227A PHE* 3.5 22.6 - - - -
229A SER* 4.2 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 182 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A HIS* 5.3 2.9 + - - -
138A ILE 2.8 4.9 + - - -
139A ILE* 3.6 23.8 - - - +
140A ASN* 3.1 32.3 + - - -
180A ARG* 4.0 3.2 + - - -
181A VAL* 1.3 76.0 - - - +
183A LEU* 1.3 61.8 + - - +
219A LEU* 3.6 21.8 - - - +
222A GLN* 6.1 0.4 - - - -
227A PHE* 5.1 0.9 - - - -
228A ILE 3.5 23.3 - - - -
229A SER 3.3 9.0 - - - -
230A GLU* 5.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 183 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A ASN* 3.6 18.6 - - + +
142A SER* 3.9 17.3 - - - -
163A LEU* 4.9 2.5 - - + -
164A ASN* 3.4 43.7 - - + +
167A MET* 4.8 10.1 - - + -
168A THR* 4.1 22.2 - - - +
182A SER* 1.3 77.0 - - - +
184A VAL* 1.3 63.7 + - - +
185A ALA* 5.6 1.1 - - + -
229A SER 3.0 12.4 + - - +
230A GLU* 3.3 28.0 - - + +
231A VAL* 2.9 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 184 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A ILE* 4.2 13.5 - - + -
140A ASN 2.8 10.9 + - - +
141A ILE* 3.7 14.8 - - + +
142A SER* 2.8 31.2 + - - +
183A LEU* 1.3 76.6 - - - +
185A ALA* 1.3 62.1 + - - +
212A ILE* 4.5 20.6 - - + -
215A VAL* 4.0 20.6 - - + -
216A VAL* 4.7 3.4 - - + -
219A LEU* 3.7 26.7 - - + -
231A VAL* 3.5 9.0 - - + +
233A VAL* 4.3 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 185 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A SER* 3.3 15.7 - - - +
144A LEU 4.5 2.5 - - - +
145A ALA* 4.4 11.2 - - + -
164A ASN* 5.7 0.9 - - - +
183A LEU* 4.2 2.4 - - + -
184A VAL* 1.3 79.8 - - - +
186A PRO* 1.4 72.9 - - + +
230A GLU* 4.3 8.3 - - - +
231A VAL 3.1 7.3 + - - +
232A LEU* 3.2 21.0 - - + -
233A VAL* 2.8 26.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 186 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A SER 3.3 15.0 - - - +
143A SER* 3.3 28.0 - - - +
144A LEU* 3.9 6.1 - - + +
145A ALA* 3.6 20.3 - - - +
147A LYS* 3.8 4.3 + - - -
185A ALA* 1.4 88.8 - - + +
187A GLY* 1.3 59.8 + - - +
188A SER* 3.3 15.6 + - - +
207A ILE* 4.3 15.3 - - + -
232A LEU* 4.1 2.2 - - - +
233A VAL 3.2 10.5 - - - +
235A PRO* 6.3 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