Contacts of the strand formed by residues 203 - 209 (chain F) in PDB entry 6K7O
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 203 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147F LEU* 4.4 30.5 - - + -
163F TRP* 4.2 7.6 - + + -
164F ASN* 3.1 25.8 - - - -
168F LEU* 3.5 32.1 - - + +
191F VAL* 5.2 3.6 - - + -
193F VAL* 3.9 19.2 - - + +
197F SER* 3.5 44.2 + - - -
198F LEU* 5.3 3.6 - - + -
201F GLN* 3.7 20.8 + - + +
202F THR* 1.3 75.8 + - - +
204F ILE* 1.3 62.2 + - - +
219F LYS* 4.8 0.3 - - - +
220F VAL* 3.4 36.5 + - + +
221F GLU* 5.4 0.4 + - - -
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Residues in contact with ILE 204 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163F TRP* 3.3 5.1 - - - -
164F ASN* 2.5 43.4 + - - +
202F THR* 3.8 22.2 - - + +
203F TYR* 1.3 78.8 - - - +
205F CYS* 1.3 62.2 + - - +
206F ASN* 3.4 7.6 + - - +
217F ASP* 3.6 17.7 - - + +
218F LYS 3.2 33.4 - - - +
219F LYS* 3.8 24.5 - - + +
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Residues in contact with CYS 205 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130F VAL* 3.6 18.4 - - - -
149F CYS* 2.0 52.3 - - + -
161F VAL* 4.2 12.6 - - + -
162F SER 3.6 4.3 - - - -
163F TRP* 3.2 20.3 - - + -
204F ILE* 1.3 72.8 - - - +
206F ASN* 1.3 59.9 + - - +
207F VAL* 4.2 3.6 - - - -
216F VAL 3.6 1.2 - - - +
217F ASP* 3.2 4.5 - - - -
218F LYS* 3.0 31.8 + - - -
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Residues in contact with ASN 206 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160F THR 3.4 1.7 - - - +
161F VAL* 3.1 4.4 - - - -
162F SER* 2.6 55.9 + - - +
164F ASN* 4.0 1.2 - - - +
165F SER* 3.5 34.2 + - - +
204F ILE* 3.4 21.8 + - - +
205F CYS* 1.3 71.6 + - - +
207F VAL* 1.3 62.9 + - - +
208F ASN* 5.4 0.7 - - - +
215F LYS* 5.0 8.0 - - + -
217F ASP* 2.8 33.8 - - - +
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Residues in contact with VAL 207 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128F PRO* 4.2 24.9 - - + -
130F VAL* 3.9 36.1 - - + -
151F VAL* 3.9 16.6 - - + -
159F VAL* 4.8 4.7 - - + -
160F THR 3.2 7.6 - - - +
161F VAL* 3.7 22.4 - - + -
205F CYS* 4.2 10.1 - - - -
206F ASN* 1.3 74.8 - - - +
208F ASN* 1.3 66.0 + - - +
209F HIS 4.9 0.2 - - - +
214F THR 3.8 0.6 - - - +
215F LYS* 3.2 3.7 - - - +
216F VAL* 2.5 46.4 + - + +
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Residues in contact with ASN 208 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158F PRO 4.6 0.2 - - - +
159F VAL* 3.8 1.0 - - - -
160F THR* 2.8 53.3 + - - +
206F ASN 5.4 0.4 - - - +
207F VAL* 1.3 76.2 - - - +
209F HIS* 1.3 60.0 + - - +
210F LYS* 3.7 32.4 + - - +
213F ASN* 4.9 1.4 - - - -
214F THR 3.0 18.1 + - - +
215F LYS* 3.4 33.5 - - + +
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Residues in contact with HIS 209 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125F THR* 4.0 0.2 - - + -
126F LYS 3.5 8.8 + - - -
128F PRO* 3.6 24.8 - - + +
154F TYR* 3.8 7.9 - + + -
155F PHE 3.2 24.1 + - - -
156F PRO 2.6 28.3 + - - -
158F PRO 3.7 8.5 - - - -
159F VAL* 3.4 26.0 - - + -
207F VAL* 4.9 0.4 - - - +
208F ASN* 1.3 70.3 - - - +
210F LYS* 1.3 64.5 + - - +
211F PRO* 3.6 19.3 - - + +
212F SER* 2.3 44.0 + - - +
214F THR 2.6 24.7 + - - +
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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