Contacts of the strand formed by residues 254 - 260 (chain C) in PDB entry 5D7I
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 254 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198C LEU* 4.2 8.1 - - + -
214C TRP* 4.0 17.0 - - + -
215C MET 3.3 7.4 - - - +
216C LYS* 3.7 15.3 - - + -
221C ILE* 3.6 26.7 - - + -
244C ILE* 3.4 17.7 - - + -
245C GLU 4.9 5.6 + - - -
246C LEU* 3.4 32.3 - - + +
247C ASP* 5.2 6.6 + - - +
250C SER* 4.4 3.6 + - - -
252C ASN* 3.1 44.3 + - + +
253C LEU* 1.3 74.4 - - - +
255C SER* 1.3 62.7 + - - +
268C GLN* 4.1 0.5 - - - +
269C VAL* 2.8 35.1 + - - +
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Residues in contact with SER 255 (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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214C TRP* 3.3 8.8 - - - -
215C MET* 3.0 37.0 + - - +
218C GLY* 5.5 3.6 + - - -
254C TYR* 1.3 76.4 - - - +
256C CYS* 1.3 61.3 + - - +
257C HIS* 3.0 22.7 + - - -
266C VAL* 3.9 13.2 - - - +
267C LEU 3.2 13.0 - - - -
268C GLN* 3.9 11.0 - - - -
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Residues in contact with CYS 256 (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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184C VAL* 4.8 0.7 - - - -
186C VAL* 4.3 4.9 - - + -
200C CYS* 2.0 55.4 - - + -
212C MET* 4.4 2.9 - - - -
213C THR 3.5 11.4 - - - -
214C TRP* 3.5 15.7 - - + -
242C ALA* 6.0 0.4 - - - -
255C SER* 1.3 72.8 - - - +
257C HIS* 1.3 64.6 + - - +
258C VAL* 3.9 15.0 - - - -
265C MET 3.7 0.9 - - - +
266C VAL* 3.3 5.0 - - - -
267C LEU* 2.8 42.0 + - + +
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Residues in contact with HIS 257 (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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211C TYR 3.6 1.5 - - - +
212C MET* 3.3 4.0 - - - -
213C THR* 2.8 49.0 + - + +
215C MET* 3.5 42.6 - - + +
218C GLY* 5.9 0.8 - - - -
255C SER* 3.0 33.4 + - - -
256C CYS* 1.3 77.1 - - - +
258C VAL* 1.3 63.1 + - - +
264C HIS* 3.0 30.1 + + + +
265C MET 3.4 3.8 - - - -
266C VAL* 3.6 22.2 - - + +
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Residues in contact with VAL 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182C PRO* 4.3 15.0 - - + -
184C VAL* 4.0 23.3 - - + -
210C ILE* 3.7 32.3 - - + -
211C TYR 3.2 3.4 - - - +
212C MET* 4.1 15.9 - - + -
256C CYS* 3.9 18.8 - - - -
257C HIS* 1.3 79.9 - - - +
259C GLU* 1.3 65.8 + - - +
260C HIS* 4.2 0.9 - - + +
263C VAL 3.7 0.9 - - - +
264C HIS* 3.4 5.4 + - - -
265C MET* 2.8 50.9 + - + +
267C LEU* 5.3 0.9 - - + -
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Residues in contact with GLU 259 (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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210C ILE* 3.5 2.3 - - - +
211C TYR* 2.8 61.7 + - + +
258C VAL* 1.3 76.5 - - - +
260C HIS* 1.3 68.0 + - - +
261C SER 5.3 0.4 + - - +
262C GLY* 4.9 9.4 + - - +
263C VAL 3.4 15.3 - - - +
264C HIS* 3.8 21.1 + - + +
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Residues in contact with HIS 260 (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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179C THR* 4.2 5.7 - - + +
180C GLU 3.5 14.8 - - - -
181C PRO* 4.2 2.6 - - - +
182C PRO* 3.6 27.6 - - + +
205C PHE* 3.9 14.5 - + + +
206C TYR 3.2 23.9 - - - -
207C PRO* 2.9 30.0 + - + +
209C GLU 3.1 26.5 - - - -
210C ILE* 4.0 9.6 - - + -
211C TYR* 5.5 1.1 - - - -
258C VAL* 4.2 1.3 - - + -
259C GLU* 1.3 77.6 - - - +
261C SER* 1.3 77.9 - - - +
262C GLY 3.3 1.3 - - - -
263C VAL* 2.9 25.9 + - - +
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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