Contacts of the strand formed by residues 192 - 197 (chain I) in PDB entry 3KYM
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 TYR 192 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117I ILE* 3.3 15.8 - - + +
132I VAL* 4.5 21.3 - - + -
148I TRP* 5.2 1.1 - - + -
150I VAL* 3.4 26.5 - - + -
155I GLN* 4.4 4.5 - - - -
179I LEU* 4.5 4.7 - - + -
181I LEU* 3.9 17.7 - - + +
185I ASP 4.3 0.9 + - - -
186I TYR* 2.3 66.0 + + - -
189I HIS* 3.8 33.4 - + + +
190I LYS 4.4 0.2 - - - -
191I VAL* 1.3 77.5 - - - +
193I ALA* 1.3 54.8 + - - +
208I SER* 2.6 22.1 + - - -
209I PHE 2.9 21.5 + - - +
211I ARG* 3.9 10.1 - - + -
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Residues in contact with ALA 193 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117I ILE* 4.5 0.4 - - - -
148I TRP* 3.4 19.5 - - - -
149I LYS* 2.9 46.3 + - + +
150I VAL* 3.7 2.1 - - - +
191I VAL 4.9 2.9 - - - +
192I TYR* 1.3 76.2 - - - +
194I CYS* 1.3 62.6 + - - +
195I GLU 4.2 0.2 - - - -
206I THR* 5.5 9.0 - - + -
207I LYS 3.6 2.5 - - - +
208I SER* 3.4 17.7 - - - +
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Residues in contact with CYS 194 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115I VAL* 4.6 0.6 - - - +
117I ILE* 4.5 9.9 - - + -
134I CYS* 2.0 53.4 - - + -
146I VAL* 3.7 22.2 - - - -
147I GLN 3.7 3.1 - - - -
148I TRP* 4.5 10.1 - - + -
193I ALA* 1.3 76.3 - - - +
195I GLU* 1.3 60.4 + - - +
196I VAL* 4.1 6.0 + - - +
205I VAL 3.8 2.6 - - - +
206I THR* 3.7 1.1 - - - -
207I LYS* 2.8 37.2 + - + +
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Residues in contact with GLU 195 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145I LYS 3.5 1.4 - - - +
146I VAL* 3.3 3.3 - - - -
147I GLN* 2.5 76.9 + - + +
149I LYS* 4.7 5.8 - - + +
193I ALA 4.2 0.4 - - - -
194I CYS* 1.3 70.4 - - - +
196I VAL* 1.3 73.5 + - - +
197I THR* 4.2 2.8 + - - +
204I PRO* 3.1 20.2 - - + +
205I VAL 2.7 32.0 + - - +
206I THR* 2.4 52.7 - - + +
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Residues in contact with VAL 196 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113I PRO* 5.2 6.7 - - + -
115I VAL* 3.9 23.3 - - + -
136I LEU* 3.0 46.9 - - + -
144I ALA* 5.3 1.8 - - + -
145I LYS 3.4 3.6 - - - +
146I VAL* 3.7 16.6 - - + -
194I CYS* 4.1 3.8 - - - -
195I GLU* 1.3 92.5 + - - +
197I THR* 1.3 69.2 + - - +
198I HIS* 3.9 10.1 + - + +
204I PRO* 3.7 12.6 - - - +
205I VAL* 3.8 8.3 + - + +
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Residues in contact with THR 197 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143I GLU* 4.9 7.2 - - - +
144I ALA* 3.2 10.9 - - - +
145I LYS* 2.9 63.0 + - + +
195I GLU* 4.2 2.5 + - - +
196I VAL* 1.3 72.7 - - - +
198I HIS* 1.3 65.4 + - - +
204I PRO* 4.4 18.1 - - + +
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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
------------------------------------------------------------
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