Contacts of the strand formed by residues 183 - 190 (chain A) in PDB entry 6KSF
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 LYS 183 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A TYR* 3.5 7.2 - - - -
178A ASN* 3.0 30.7 + - - +
181A SER* 3.0 25.2 - - - +
182A LYS* 1.3 83.8 - - - +
184A TYR* 1.3 68.1 + - - +
185A SER* 5.1 0.2 - - - -
235A CYS* 5.5 0.4 - - - -
236A GLU* 3.6 17.7 - - + +
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Residues in contact with TYR 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A TYR* 3.8 16.4 - - + -
176A HIS 3.6 18.6 - - - -
177A TYR* 3.6 32.8 - + + -
183A LYS* 1.3 83.6 - - - +
185A SER* 1.3 63.0 + - - +
216A ALA* 3.7 18.7 - - + +
218A ILE* 5.4 0.9 - - - +
235A CYS* 4.5 4.0 - - + -
237A LEU* 4.2 23.6 - - + -
344A ARG* 3.7 12.8 + - - -
346A VAL* 3.6 35.0 - - + -
353A PHE* 3.1 30.7 - - + -
10B C 4.6 1.2 + - - -
101B XL3 3.3 27.0 - - - +
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Residues in contact with SER 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A TYR* 3.4 23.4 - - - +
176A HIS 3.5 15.3 + - - +
178A ASN* 5.6 7.8 + - - +
183A LYS 5.1 1.6 - - - -
184A TYR* 1.3 78.3 - - - +
186A ALA* 1.3 61.3 + - - +
187A ASP* 3.1 36.4 + - - +
189A TYR* 5.3 0.7 - - - +
353A PHE* 3.8 10.1 - - - -
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Residues in contact with ALA 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A TYR* 4.2 13.2 - - + -
185A SER* 1.3 73.6 - - - +
187A ASP* 1.3 65.2 + - - +
188A HIS 3.1 3.3 + - - -
189A TYR* 3.2 19.1 + - + +
353A PHE* 4.2 29.8 - - + +
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Residues in contact with ASP 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A HIS* 4.4 9.9 + - - +
185A SER* 3.1 26.0 + - - +
186A ALA* 1.3 75.1 - - - +
188A HIS* 1.3 79.1 + - + +
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Residues in contact with HIS 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A VAL* 6.4 0.9 - - + -
176A HIS* 2.9 35.1 + - + +
186A ALA 3.1 2.0 + - - -
187A ASP* 1.3 80.1 + - + +
189A TYR* 1.3 62.1 + - - +
190A THR* 4.2 3.7 - - + +
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Residues in contact with TYR 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A GLY* 3.5 35.7 - - - -
175A TYR* 3.7 40.1 - + + +
176A HIS* 5.6 0.7 - - - +
185A SER 5.6 0.2 - - - -
186A ALA* 3.2 23.5 + - + +
187A ASP 4.6 0.2 - - - -
188A HIS* 1.3 76.2 - - - +
190A THR* 1.3 67.9 + - - +
191A PRO* 3.6 20.4 - - + +
192A PHE* 3.4 19.2 + - + +
215A GLU* 4.8 0.7 - - - -
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Residues in contact with THR 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A PRO* 3.3 32.3 - - + +
127A ASN* 4.1 16.0 + - - -
128A VAL* 4.7 4.5 - - + -
172A THR 4.3 5.0 + - - -
174A GLY* 3.0 32.0 + - - -
176A HIS* 3.8 18.7 + - + -
188A HIS* 3.7 8.0 + - + +
189A TYR* 1.3 83.8 - - - +
191A PRO* 1.3 74.6 - - - +
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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