Contacts of the strand formed by residues 181 - 187 (chain B) in PDB entry 1K4R
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 ASP 181 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173B ILE* 3.9 22.1 - - + +
174B LEU 3.2 5.6 - - - +
175B THR* 2.7 36.5 + - - +
180B GLY* 1.3 75.7 - - - -
182B VAL* 1.3 60.6 + - - +
293B GLY 4.5 1.4 - - - +
296B LYS* 3.2 43.6 + - + +
297B LEU* 3.7 6.4 + - - +
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Residues in contact with VAL 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B MET* 4.2 8.1 - - + -
143B VAL* 4.7 7.9 - - + -
172B THR 4.0 0.3 - - - +
173B ILE* 3.4 4.3 - - - +
174B LEU* 2.8 52.7 + - + +
176B MET* 3.7 24.2 - - + -
180B GLY 4.1 0.4 + - - -
181B ASP* 1.3 74.4 - - - +
183B SER* 1.3 65.1 + - - +
184B LEU* 4.1 4.4 + - + -
292B VAL* 3.6 24.2 - - + -
293B GLY 3.4 15.5 - - - +
294B LEU* 4.6 0.4 - - + -
297B LEU* 4.2 21.3 - - + -
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Residues in contact with SER 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B ARG* 5.9 1.2 + - - -
171B LYS* 4.3 14.8 - - - -
172B THR 3.5 4.0 - - - -
173B ILE* 3.8 22.2 - - - +
182B VAL* 1.3 74.9 - - - +
184B LEU* 1.3 61.6 + - - +
185B LEU 4.2 0.4 - - - -
291B GLU 3.5 1.1 + - - +
292B VAL* 3.4 7.4 - - - +
293B GLY* 2.9 46.9 + - - -
295B GLU* 4.2 6.1 + - - -
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Residues in contact with LEU 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B VAL* 4.9 6.7 - - + -
141B VAL* 4.1 17.3 - - + -
143B VAL* 3.9 26.7 - - + -
163B ALA* 4.0 23.8 - - + -
165B PHE* 3.5 16.4 - - + -
171B LYS* 3.3 5.5 - - - +
172B THR* 2.8 41.1 + - - +
174B LEU* 4.1 8.3 - - + -
182B VAL* 4.1 5.1 + - + +
183B SER* 1.3 77.3 - - - +
185B LEU* 1.3 60.7 + - - +
186B CYS* 3.9 2.7 - - - -
290B CYS* 4.5 11.2 - - + -
291B GLU 3.5 2.0 - - - +
292B VAL* 3.8 32.1 - - + -
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Residues in contact with LEU 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B ARG* 4.5 12.8 - - - +
170B GLU* 3.2 28.7 - - + +
171B LYS* 4.3 25.6 - - + +
183B SER 4.2 0.4 - - - -
184B LEU* 1.3 73.8 - - - +
186B CYS* 1.3 60.4 + - - +
187B ARG* 3.7 51.7 + - + +
289B THR 4.0 0.7 - - - +
290B CYS* 3.1 2.1 - - - -
291B GLU* 2.8 53.2 + - + +
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Residues in contact with CYS 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B TYR* 6.1 0.9 - - + -
141B VAL* 4.1 4.9 - - - -
165B PHE* 3.5 47.7 - - + +
166B THR 5.3 0.3 - - - +
170B GLU* 3.0 26.8 + - - +
184B LEU* 3.9 6.2 - - - -
185B LEU* 1.3 75.9 - - - +
187B ARG* 1.3 63.9 + - - +
188B VAL* 3.6 3.2 + - - +
288B VAL* 4.4 9.6 - - + -
289B THR 3.5 4.7 - - - +
290B CYS* 2.0 45.5 - - - -
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Residues in contact with ARG 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B ARG* 5.8 0.4 - - - +
170B GLU* 4.0 20.7 + - - +
185B LEU* 3.7 35.9 + - + +
186B CYS* 1.3 71.0 - - - +
188B VAL* 1.3 58.8 + - - +
189B ALA* 3.1 8.7 - - + +
190B SER* 2.6 44.2 + - - +
288B VAL* 3.3 6.5 - - - +
289B THR* 3.3 15.9 + - - +
291B GLU* 3.2 30.7 + - - +
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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