Contacts of the strand formed by residues 211 - 217 (chain C) in PDB entry 5I75
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 SER 211 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170C ILE 2.8 17.1 - - - +
171C ASP* 3.2 11.3 + - - +
209C HIS* 6.3 0.2 - - - -
210C ASN* 1.3 75.9 - - - +
212C TYR* 1.3 62.5 + - - +
213C THR* 4.4 5.0 + - - -
228C SER* 5.6 3.8 - - - -
229C PHE 2.8 11.9 - - - -
230C ASN* 3.3 22.7 - - - -
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Residues in contact with TYR 212 (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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137C ILE* 4.3 2.5 - - + -
152C VAL* 3.9 23.6 - - + -
168C TRP* 5.6 1.8 - + + -
169C LYS 4.9 0.2 - - - -
170C ILE* 3.7 42.0 - - + -
199C LEU* 4.8 5.6 - - + -
201C LEU* 4.6 15.1 - - + +
205C GLU 4.3 1.4 + - - -
206C TYR* 3.3 53.4 + + - -
209C HIS* 4.0 19.2 - - + +
210C ASN 3.9 11.9 - - - -
211C SER* 1.3 70.6 - - - +
213C THR* 1.3 65.1 + - - +
228C SER* 3.0 6.2 - - - -
229C PHE* 2.9 63.8 + + + -
231C ARG* 5.3 0.7 - - + -
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Residues in contact with THR 213 (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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137C ILE* 4.5 1.3 - - - -
168C TRP* 4.6 3.1 - - - -
169C LYS* 2.7 63.5 + - + +
170C ILE 5.5 0.2 - - - -
172C GLY 6.1 0.9 - - - -
211C SER* 4.4 5.3 + - - -
212C TYR* 1.3 76.4 + - - +
214C CYS* 1.3 63.1 + - - +
215C GLU 5.0 0.2 - - - +
226C VAL* 3.5 21.5 - - + -
227C LYS 3.0 9.2 - - - +
228C SER* 2.4 30.3 + - - +
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Residues in contact with CYS 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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135C VAL* 4.2 5.8 - - - +
137C ILE* 3.7 25.0 - - - +
154C CYS* 2.0 52.9 - - + -
166C VAL* 5.7 1.3 - - + -
167C LYS 3.8 6.1 - - - +
168C TRP* 4.0 20.9 - - + +
213C THR* 1.3 74.6 - - - +
215C GLU* 1.3 61.5 + - - +
225C ILE 3.7 0.9 - - - +
227C LYS* 2.9 31.1 + - - +
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Residues in contact with GLU 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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135C VAL* 5.9 0.7 - - - -
154C CYS* 5.9 1.3 - - - -
166C VAL* 3.8 4.8 - - - +
167C LYS* 2.9 69.5 + - + +
169C LYS* 3.2 39.4 + - + -
213C THR* 4.3 1.8 - - + -
214C CYS* 1.3 75.2 - - - +
216C ALA* 1.3 61.9 + - - +
217C THR* 5.5 1.7 + - - +
224C PRO* 4.1 19.3 - - + +
225C ILE 2.9 12.1 - - - +
226C VAL* 3.5 24.9 - - + +
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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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133C PRO* 5.3 3.6 - - + +
135C VAL* 4.1 18.6 - - + +
154C CYS* 6.3 0.7 - - - -
156C LEU* 3.6 32.3 - - + -
164C ILE* 4.3 6.5 - - + -
165C ASN 3.4 8.1 - - - +
166C VAL* 4.8 1.6 - - + -
215C GLU* 1.3 76.0 - - - +
217C THR* 1.3 62.0 + - - +
218C HIS* 4.0 2.4 + - - +
224C PRO* 3.1 3.8 - - - +
225C ILE* 2.9 33.3 + - + +
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Residues in contact with THR 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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164C ILE* 3.3 3.8 - - - +
165C ASN* 2.9 58.4 + - + +
167C LYS* 5.9 2.8 - - - +
215C GLU* 5.5 2.3 + - - +
216C ALA* 1.3 70.3 - - - +
218C HIS* 1.3 68.5 + - - +
221C SER 5.4 0.4 - - - +
222C THR* 5.0 7.0 - - - +
224C PRO* 3.2 31.1 - - + +
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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