Contacts of the strand formed by residues 194 - 200 (chain C) in PDB entry 6H25
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 VAL 194 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32C PHE* 6.0 1.3 - - + -
150C ASP* 4.9 4.5 - - - +
153C THR* 5.0 1.8 - - + -
154C PHE* 5.3 8.3 - - + +
157C LEU* 4.2 13.0 - - + -
192C HIS* 4.2 1.8 - - + +
193C PRO* 1.3 79.4 - - - +
195C ALA* 1.3 72.1 + - - +
196C THR* 4.1 6.3 + - + +
224C ILE 3.7 1.2 - - - +
225C VAL* 3.3 2.8 - - - -
226C MET* 2.9 31.3 + - - +
258C ARG* 4.9 1.8 - - + +
259C HIS* 3.4 37.4 - - + +
262C VAL* 3.7 35.2 - - + -
263C LYS* 6.4 0.2 - - + -
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Residues in contact with ALA 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C PHE* 5.0 0.5 - - - -
108C PHE* 4.8 3.4 - - + -
149C LEU 4.8 1.8 - - - +
150C ASP* 2.9 33.0 - - + +
153C THR* 3.7 27.4 - - + +
194C VAL* 1.3 78.7 - - - +
196C THR* 1.3 66.2 + - - +
197C SER* 5.1 0.7 - - - +
223C THR* 4.5 11.0 - - + -
224C ILE 3.2 5.6 - - - +
225C VAL* 3.7 22.2 - - + +
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Residues in contact with THR 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C PHE* 4.6 11.7 - - + -
150C ASP* 4.8 3.1 - - - -
194C VAL* 4.1 6.7 + - + +
195C ALA* 1.3 79.5 - - - +
197C SER* 1.3 63.6 + - - +
198C PHE* 4.2 20.4 + - - -
208C VAL* 5.8 1.3 - - - -
222C LEU* 5.4 0.7 - - - +
223C THR* 3.6 0.3 - - - -
224C ILE* 2.9 32.9 + - - +
255C ALA* 3.4 30.9 - - + +
258C ARG* 3.7 34.1 - - + -
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Residues in contact with SER 197 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C PHE* 6.1 0.2 - - - -
147C ASN* 3.3 38.2 + - - +
149C LEU* 4.4 5.4 - - - +
150C ASP 4.9 1.0 + - - -
195C ALA* 5.1 1.2 - - - +
196C THR* 1.3 71.8 - - - +
198C PHE* 1.3 66.7 + - - +
208C VAL* 4.7 1.0 - - - +
209C ASP* 3.3 22.7 + - - -
210C PRO* 4.1 3.3 - - - +
221C THR* 5.4 4.7 - - - -
222C LEU 3.2 11.4 - - - -
223C THR* 2.9 27.7 + - - +
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Residues in contact with PHE 198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196C THR* 4.2 23.8 + - - -
197C SER* 1.3 83.6 - - - +
199C ALA* 1.3 62.7 + - - +
200C VAL* 5.0 2.0 - - + -
206C LEU* 3.9 16.4 - - + -
207C ILE 3.3 8.3 - - - +
208C VAL* 3.6 39.3 - - + -
210C PRO* 4.8 3.5 - - - +
221C THR* 3.6 6.6 - - - +
222C LEU* 2.9 48.4 + - + +
224C ILE* 5.4 1.3 - - + -
251C CYS* 3.5 56.1 - - + -
254C ARG* 4.5 19.3 - - + -
255C ALA* 5.1 0.9 - - - -
258C ARG* 6.1 0.7 - - - -
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Residues in contact with ALA 199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198C PHE* 1.3 74.1 - - - +
200C VAL* 1.3 61.9 + - - +
201C PHE 4.0 0.5 + - - -
206C LEU* 3.4 2.8 - - - -
207C ILE* 2.9 54.0 + - + +
210C PRO* 3.7 28.6 - - + +
215C GLU* 5.2 4.3 - - + -
218C ALA* 4.5 13.5 - - + -
220C GLY 3.6 7.4 - - - +
221C THR* 4.8 1.1 - - - +
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Residues in contact with VAL 200 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198C PHE* 4.9 1.3 - - + +
199C ALA* 1.3 77.3 - - - +
201C PHE* 1.3 76.0 + - - +
204C THR* 5.4 4.5 - - - -
205C LEU 4.3 2.9 - - - +
206C LEU* 4.4 17.9 - - + +
218C ALA* 4.2 1.4 - - - +
219C THR* 2.9 25.6 + - - -
220C GLY* 2.9 29.5 + - - +
221C THR 5.3 0.2 - - - -
222C LEU* 4.8 22.7 - - + -
237C LYS* 5.4 7.4 - - - -
240C GLY 5.3 2.2 - - - +
241C SER* 4.6 15.9 - - - +
242C GLY 5.0 9.4 - - - +
243C LEU* 5.3 11.4 - - + -
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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