Contacts of the strand formed by residues 212 - 215 (chain A) in PDB entry 5M7T
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 PHE 212 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158A LEU* 5.7 0.9 - - + -
169A PHE* 3.3 33.7 - - + -
170A ALA* 4.6 2.7 - - - -
171A LEU* 4.3 15.3 - - + -
199A THR* 3.9 23.6 - - + -
202A ILE* 4.0 18.8 - - + -
203A TYR* 3.7 36.6 - + + -
206A LEU* 3.9 16.2 - - + -
209A PRO* 3.9 17.4 + - + -
210A GLU 4.2 1.4 + - - -
211A THR* 1.3 74.0 - - - +
213A LEU* 1.3 77.0 + - - +
244A GLY 4.9 3.2 + - - +
245A ILE* 3.5 21.1 - - + +
246A GLU* 3.0 26.7 + - - +
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Residues in contact with LEU 213 (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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61A LEU* 4.1 9.9 - - + -
94A LEU* 4.1 15.9 - - + -
134A ILE* 3.8 24.0 - - + -
169A PHE 3.0 11.6 + - - +
170A ALA* 3.1 11.9 - - + -
171A LEU 2.9 25.0 + - - -
211A THR* 3.9 17.3 - - + -
212A PHE* 1.3 89.4 - - - +
214A PHE* 1.3 59.9 + - - +
215A CYS 4.3 0.2 - - - -
245A ILE* 4.4 0.2 - - - -
246A GLU* 3.5 24.2 - - + +
248A LEU* 4.1 19.7 - - + -
276A VAL* 4.8 5.4 - - + -
311A LEU* 4.1 20.4 - - + -
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Residues in contact with PHE 214 (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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171A LEU 3.4 3.8 - - - -
173A PHE* 3.6 24.9 - + - -
195A GLN* 3.5 31.2 - - + -
196A VAL* 4.8 4.5 - - + -
199A THR* 3.5 35.2 - - + -
213A LEU* 1.3 76.2 - - - +
215A CYS* 1.3 58.1 + - - +
216A PRO* 3.8 24.9 - - + +
233A TYR* 4.1 2.2 - - - -
237A VAL* 4.0 27.8 - - + -
241A LEU* 4.0 17.7 - - + -
245A ILE* 3.9 14.6 - - + -
246A GLU 3.0 11.9 + - - +
247A VAL* 3.5 6.7 - - + -
248A LEU* 2.9 25.5 + - - -
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Residues in contact with CYS 215 (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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171A LEU 3.0 8.5 + - - -
172A LEU* 3.7 27.1 - - + -
173A PHE* 2.9 28.9 + - - +
174A ASP* 3.8 22.9 - - - -
214A PHE* 1.3 74.8 - - - +
216A PRO* 1.4 77.2 - - - +
219A TYR* 4.0 10.8 - - - -
248A LEU* 3.8 18.0 - - + +
278A TRP* 5.0 3.8 - - - -
1001A GDV 4.5 9.6 - - - -
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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