Contacts of the strand formed by residues 268 - 273 (chain A) in PDB entry 3SPC
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 ILE 268 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A ARG* 3.4 4.0 - - - -
215A VAL* 2.9 36.3 + - + +
262A ILE* 4.5 16.2 - - + -
263A PHE 3.5 28.3 - - - +
264A LEU* 3.9 16.8 - - + +
265A VAL 5.2 0.2 - - - +
266A SER* 3.4 13.0 + - - +
267A PRO* 1.3 75.0 - - - +
269A THR* 1.3 76.7 + - - +
270A ILE* 4.2 13.5 - - + -
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Residues in contact with THR 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A ARG* 4.2 19.0 + - - +
212A MET* 3.9 37.7 - - + -
213A TRP 3.5 6.7 - - - +
214A ARG* 4.3 15.7 + - - +
268A ILE* 1.3 82.4 - - - +
270A ILE* 1.3 62.7 + - - +
271A LEU* 3.7 11.4 + - + +
327A PHE* 4.2 20.6 - - + +
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Residues in contact with ILE 270 (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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211A LEU 3.8 0.5 - - - +
212A MET* 3.2 27.2 - - - +
213A TRP* 2.7 62.0 + - + +
215A VAL* 4.1 25.4 - - + -
228A VAL* 3.9 35.0 - - + -
253A VAL* 3.8 17.7 - - + +
262A ILE* 4.4 10.3 - - + -
268A ILE* 4.2 13.5 - - + -
269A THR* 1.3 72.5 - - - +
271A LEU* 1.3 61.1 + - - +
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Residues in contact with LEU 271 (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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205A ARG* 3.5 38.1 - - + +
210A CYS* 4.2 15.3 - - + -
211A LEU 3.7 0.4 - - - -
212A MET* 3.2 43.7 - - + -
252A ASP 4.2 0.2 - - - +
253A VAL* 3.9 25.7 - - - +
269A THR* 3.7 9.6 + - + +
270A ILE* 1.3 78.1 - - - +
272A HIS* 1.3 61.3 + - - +
273A GLU* 4.0 5.0 + - + +
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Residues in contact with HIS 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A CYS* 3.2 5.2 - - - -
211A LEU* 2.8 54.3 + - + +
213A TRP* 4.3 8.5 - - + -
251A ILE* 3.3 27.5 - - + +
252A ASP* 2.8 44.1 + - + +
253A VAL* 4.5 0.2 - - + -
271A LEU* 1.3 72.7 - - - +
273A GLU* 1.3 75.2 + - - +
274A ILE* 3.4 12.6 + - + -
275A ASN* 5.8 0.2 - - - -
278A SER* 2.7 36.3 + - - -
279A PRO* 4.4 3.5 - - + +
280A LEU* 4.1 8.2 - - + +
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Residues in contact with GLU 273 (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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208A LYS* 3.2 44.9 + - + +
209A LEU 4.0 5.4 - - - +
210A CYS* 4.0 17.0 - - - -
252A ASP* 4.5 2.7 + - - +
271A LEU* 4.0 6.1 + - + +
272A HIS* 1.3 88.9 + - - +
274A ILE* 1.3 62.0 + - - +
275A ASN* 3.5 23.3 + - + +
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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