Contacts of the strand formed by residues 213 - 220 (chain C) in PDB entry 3B4M
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 213 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178C ASN* 3.3 52.9 - - - +
179C VAL 3.4 11.0 - - - +
181C TYR 4.3 0.4 - - - +
205C CYS* 4.6 8.8 - - - -
206C ASP 5.1 2.3 + - - -
207C LYS* 5.2 4.7 + - - +
212C PRO* 1.3 78.8 - - + +
214C GLY* 1.3 62.3 + - - +
240C ARG* 3.4 28.9 - - - +
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Residues in contact with GLY 214 (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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178C ASN* 3.5 7.4 + - - -
179C VAL* 2.7 30.1 + - - -
180C ASP 4.9 0.2 - - - -
181C TYR 4.8 0.4 - - - +
203C ILE* 6.4 0.2 - - - -
204C LEU 3.5 11.0 - - - -
205C CYS* 4.3 13.0 - - - -
206C ASP 5.2 1.1 - - - -
213C LYS* 1.3 76.8 + - - +
215C PHE* 1.3 70.5 + - - +
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Residues in contact with PHE 215 (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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175C TYR* 3.3 36.1 - + + +
176C VAL 3.1 14.8 - - - +
177C GLY* 4.1 0.7 - - - -
179C VAL* 3.7 7.5 - - - +
203C ILE* 3.5 5.6 - - - +
204C LEU* 2.7 73.5 + - + +
206C ASP* 4.3 7.6 - - - -
214C GLY* 1.3 79.3 - - - +
216C ALA* 1.3 60.4 + - - +
217C TYR* 3.7 23.6 - + - -
200D ARG* 3.9 27.4 - - - -
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Residues in contact with ALA 216 (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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175C TYR* 3.6 2.4 - - - -
176C VAL* 2.7 47.1 + - + +
179C VAL* 3.9 11.9 - - + -
188C LEU* 3.7 31.0 - - + -
201C VAL* 5.1 0.2 - - + -
202C THR 2.9 12.6 - - - +
203C ILE* 4.5 1.6 - - + -
204C LEU* 4.7 0.7 - - - -
215C PHE* 1.3 76.9 - - - +
217C TYR* 1.3 67.1 + - - +
218C ILE* 4.2 2.0 - - + -
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Residues in contact with TYR 217 (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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173C SER* 5.1 3.4 - - - +
174C ILE 3.4 10.8 - - - +
175C TYR* 3.6 26.6 - + + -
200C ARG 3.7 1.1 - - - +
201C VAL* 3.5 2.9 - - - +
202C THR* 2.8 46.8 + - + +
204C LEU* 3.7 33.2 - - + -
215C PHE* 3.7 18.7 - + - -
216C ALA* 1.3 73.8 - - - +
218C ILE* 1.3 67.4 + - - +
219C GLU* 4.0 0.4 - - + -
247C LYS* 3.7 48.2 - - + +
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Residues in contact with ILE 218 (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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172C ARG 4.0 0.7 - - - +
173C SER* 3.1 4.3 - - - -
174C ILE* 2.8 44.5 + - + +
176C VAL* 3.8 16.4 - - + -
188C LEU* 4.2 17.5 - - + +
189C GLU* 6.0 0.7 - - - -
192C PHE* 3.5 41.1 - - + -
198C VAL* 4.2 18.2 - - + -
200C ARG 3.7 1.8 - - - -
201C VAL* 4.2 16.6 - - + -
216C ALA* 4.2 2.0 - - + -
217C TYR* 1.3 79.2 - - - +
219C GLU* 1.3 58.6 + - - +
220C PHE* 3.8 33.7 + - + -
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Residues in contact with GLU 219 (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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169C ALA* 4.1 20.0 - - - +
172C ARG* 2.7 30.2 + - + +
173C SER* 3.5 20.4 + - - +
198C VAL* 3.6 3.5 - - - +
199C ASN* 2.7 48.6 + - - +
200C ARG* 2.8 41.3 + - + +
217C TYR* 4.0 1.2 - - + +
218C ILE* 1.3 73.7 - - - +
220C PHE* 1.3 59.5 + - - +
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Residues in contact with PHE 220 (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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172C ARG* 3.2 35.0 + - - +
174C ILE* 3.8 17.5 - - + -
192C PHE* 4.2 9.0 - + + -
195C CYS* 4.0 16.2 - - + -
196C GLY 3.9 9.2 - - - -
197C SER 3.4 13.5 - - - +
198C VAL* 3.7 24.2 - - + -
199C ASN* 3.3 11.7 - - - +
218C ILE* 3.9 15.5 - - + -
219C GLU* 1.3 76.8 - - - +
221C SER* 1.3 63.3 + - - +
222C ASP 3.7 17.0 - - - +
225C SER* 3.6 17.9 - - - -
226C VAL* 3.9 8.5 - - + -
229C SER* 3.3 37.9 - - - -
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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