Contacts of the strand formed by residues 183 - 187 (chain B) in PDB entry 1KQN
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 LEU 183 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B LYS* 4.8 1.0 - - - +
153B LEU* 3.5 28.7 - - + +
155B CYS* 3.4 33.0 - - - -
159B LEU* 4.9 2.7 - - + -
160B LEU* 4.0 15.5 - - + -
163B PHE* 3.9 23.1 - - + -
177B ILE* 4.6 4.3 - - + -
178B VAL* 3.7 27.1 - - + -
182B GLY* 1.3 76.8 - - - +
184B ILE* 1.3 61.6 + - - +
185B CYS* 3.9 2.0 - - + +
209B ASN 3.1 8.2 + - - +
210B ILE* 3.4 18.6 - - + +
211B HIS* 2.7 32.2 + - - -
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Residues in contact with ILE 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LEU* 3.2 31.9 - - + -
31B ALA* 3.7 26.5 - - + -
35B MET* 3.6 38.6 - - + -
152B LYS* 4.1 13.7 - - + -
153B LEU 2.8 14.3 + - - +
154B LEU* 3.5 9.2 - - + +
155B CYS* 2.9 28.4 + - - +
183B LEU* 1.3 78.7 - - - +
185B CYS* 1.3 58.7 + - - +
186B VAL* 4.5 0.9 - - + -
211B HIS* 3.4 11.2 - - + +
213B VAL* 3.9 20.9 - - + -
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Residues in contact with CYS 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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155B CYS* 3.2 10.1 - - - +
156B GLY 3.5 6.3 - - - -
157B ALA* 3.5 40.2 - - - -
160B LEU* 3.8 26.5 - - + -
183B LEU* 3.9 3.1 - - + -
184B ILE* 1.3 72.7 - - - +
186B VAL* 1.3 57.4 + - - +
187B THR* 3.8 2.9 + - - -
193B ALA* 4.5 8.1 - - - -
210B ILE* 5.4 5.2 - - + -
211B HIS 2.7 12.8 + - - +
212B VAL* 3.3 10.8 - - + +
213B VAL 2.6 31.3 + - - +
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Residues in contact with VAL 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B LEU* 3.8 33.7 - - + +
30B LEU* 4.2 21.5 - - + -
31B ALA* 4.3 5.6 - - + +
154B LEU* 4.0 23.8 - - + -
155B CYS 2.8 8.2 + - - +
156B GLY* 3.3 7.2 - - - -
184B ILE* 4.5 0.7 - - + -
185B CYS* 1.3 71.0 - - - +
187B THR* 1.3 66.4 + - - +
213B VAL* 3.4 30.5 - - + +
215B GLU* 4.1 15.7 - - + +
755B XE 4.5 0.4 - - - -
778B NAD 2.9 20.4 - - - -
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Residues in contact with THR 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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157B ALA* 3.4 25.3 + - + +
185B CYS* 4.5 2.7 - - - +
186B VAL* 1.3 77.3 - - - +
188B ARG* 1.3 67.7 + - - +
189B ALA* 3.0 32.7 + - - +
190B GLY* 3.9 9.3 + - - -
193B ALA* 4.1 8.3 - - + -
212B VAL* 4.1 16.8 - - + -
213B VAL 2.9 8.2 + - - +
214B ASN* 3.5 4.3 - - - +
215B GLU* 3.0 30.7 + - - -
778B NAD 4.5 3.4 + - - -
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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