Contacts of the strand formed by residues 180 - 186 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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237A LEU* 3.6 22.1 - - + +
135D ARG* 6.1 2.6 - - - +
136D GLY 2.9 15.8 + - - +
137D HIS* 3.3 45.6 + - + +
138D ILE 2.9 24.2 + - - +
178D GLN 4.5 6.9 + - - +
179D VAL* 1.3 77.1 - - - +
181D VAL* 1.3 64.1 + - - +
182D SER* 4.0 1.5 + - - -
222D GLN* 3.6 18.5 + - - +
223D ALA 2.7 26.6 + - - -
224D ASP* 3.6 26.7 + - - +
226D SER 2.7 31.3 + - - -
227D PHE* 3.9 26.5 - - + +
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Residues in contact with VAL 181 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D LEU* 4.7 1.3 - - + -
138D ILE* 3.3 18.2 - - + +
140D ASN* 3.8 20.6 - - - +
167D MET* 3.5 32.5 - - + +
170D ALA* 4.2 3.4 - - + -
171D ALA* 3.7 27.5 - - - +
174D LEU* 3.7 32.1 - - + -
179D VAL* 4.0 1.0 + - + -
180D ARG* 1.3 73.4 - - - +
182D SER* 1.3 65.9 + - - +
227D PHE* 3.3 24.9 - - - -
229D SER* 4.2 3.5 - - - +
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Residues in contact with SER 182 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D HIS* 5.6 2.6 - - - -
138D ILE 2.8 7.5 + - - -
139D ILE* 3.4 26.4 - - - +
140D ASN* 2.9 34.3 + - - -
167D MET* 5.7 0.2 - - - -
180D ARG 5.0 1.9 + - - -
181D VAL* 1.3 77.7 - - - +
183D LEU* 1.3 62.2 + - - +
219D LEU* 3.6 21.3 - - - +
222D GLN* 6.1 0.2 - - - -
227D PHE* 5.0 0.2 - - - -
228D ILE 3.6 22.2 - - - -
229D SER 3.3 7.9 - - - -
230D GLU* 5.4 0.2 - - - -
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Residues in contact with LEU 183 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140D ASN* 3.5 25.6 - - + +
142D SER* 4.0 12.8 - - - -
163D LEU* 4.9 3.4 - - + -
164D ASN* 3.6 45.8 - - + +
167D MET* 4.8 11.7 - - + -
168D THR* 4.2 14.6 - - - +
182D SER* 1.3 76.0 - - - +
184D VAL* 1.3 67.2 + - - +
185D ALA* 4.3 0.7 - - + -
219D LEU* 5.0 0.3 - - - +
229D SER 2.9 12.2 + - - +
230D GLU* 3.2 30.2 - - + +
231D VAL* 2.9 26.5 + - - +
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Residues in contact with VAL 184 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139D ILE* 4.2 11.2 - - + -
140D ASN 2.9 12.9 + - - +
141D ILE* 3.7 13.0 - - + +
142D SER* 2.8 27.4 + - - +
183D LEU* 1.3 80.9 - - - +
185D ALA* 1.3 64.8 + - - +
212D ILE* 4.6 21.5 - - + -
215D VAL* 4.1 20.4 - - + -
216D VAL* 4.9 2.9 - - + -
219D LEU* 3.8 25.8 - - + -
231D VAL* 3.4 9.0 - - + +
233D VAL* 4.4 13.2 - - + -
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Residues in contact with ALA 185 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142D SER* 3.2 15.9 - - - +
144D LEU 4.4 7.2 - - - +
145D ALA* 4.4 4.5 - - - -
164D ASN* 5.6 1.8 - - - +
183D LEU* 5.4 1.6 - - + -
184D VAL* 1.3 79.7 - - - +
186D PRO* 1.3 74.1 - - + +
207D ILE* 6.0 0.4 - - - -
230D GLU* 4.2 9.6 + - - +
231D VAL 3.0 6.7 + - - -
232D LEU* 3.2 20.5 - - + -
233D VAL* 3.0 25.5 + - - +
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Residues in contact with PRO 186 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142D SER 3.2 15.3 - - - +
143D SER* 3.4 26.2 - - - +
144D LEU* 3.9 8.7 - - + +
145D ALA* 3.5 22.2 - - + +
147D LYS* 3.7 3.9 + - - +
185D ALA* 1.3 90.6 - - + +
187D GLY* 1.3 62.0 + - - +
188D SER 3.4 14.6 - - - +
207D ILE* 4.9 11.0 - - + -
232D LEU* 3.8 4.7 - - - +
233D VAL 3.5 8.1 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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