Contacts of the strand formed by residues 221 - 226 (chain C) in PDB entry 3NY5
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 GLU 221 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158C ARG* 3.2 42.3 + - - +
160C PHE* 3.8 24.6 - - + -
199C ARG* 3.8 1.4 - - - +
200C ILE* 3.3 49.4 + - + +
220C GLU* 1.3 75.2 + - - +
222C LEU* 1.3 65.0 + - - +
223C HIS* 3.9 10.3 - - + -
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Residues in contact with LEU 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157C VAL* 3.5 25.4 - - + -
158C ARG 2.7 10.3 + - - +
159C VAL* 3.4 14.9 - - + -
160C PHE* 2.8 26.7 + - - -
177C VAL* 4.3 16.4 - - + -
181C LEU* 4.7 3.1 - - + -
197C VAL* 4.1 19.7 - - + -
198C TYR 3.1 10.5 - - - +
199C ARG* 4.0 15.7 - - + -
208C ILE* 4.1 6.5 - - + -
214C ILE* 4.5 8.5 - - + -
217C LEU* 3.9 30.7 - - + -
220C GLU* 4.1 2.0 + - + -
221C GLU* 1.3 78.5 - - - +
223C HIS* 1.3 70.2 + - - +
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Residues in contact with HIS 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160C PHE* 3.3 47.7 - + + -
197C VAL* 3.3 3.5 - - - -
198C TYR* 2.7 52.3 + - + +
200C ILE* 4.1 31.0 - - + +
205C LYS* 6.0 2.0 - - + -
221C GLU* 3.9 14.1 - - + -
222C LEU* 1.3 83.6 + - - +
224C VAL* 1.3 63.3 + - - +
225C GLU* 4.2 5.4 - - + +
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Residues in contact with VAL 224 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159C VAL* 3.8 11.9 - - + -
160C PHE 2.7 15.6 + - - +
161C LEU* 3.9 9.3 - - + -
162C PRO* 3.5 26.6 - - + +
181C LEU* 3.7 29.6 - - + -
185C LEU* 4.0 20.0 - - + -
195C CYS* 3.9 22.0 - - + -
196C ALA 3.5 8.1 - - - +
197C VAL* 4.1 12.1 - - + -
210C TRP* 4.3 4.9 - - + -
223C HIS* 1.3 77.9 - - - +
225C GLU* 1.3 67.2 + - - +
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Residues in contact with GLU 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162C PRO* 4.8 1.8 - - - -
195C CYS* 3.1 7.3 - - - +
196C ALA* 2.8 35.0 + - + +
198C TYR* 3.8 37.0 + - + -
223C HIS* 4.2 4.8 + - + +
224C VAL* 1.3 79.9 - - - +
226C VAL* 1.3 65.8 + - - +
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Residues in contact with VAL 226 (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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162C PRO* 3.8 29.3 - - + +
190C LEU* 4.0 26.7 - - + -
194C CYS* 3.6 15.7 - - + +
195C CYS* 4.2 1.8 - - - -
225C GLU* 1.3 77.5 - - - +
227C LEU* 1.3 76.6 + - - +
228C GLU* 3.6 6.4 + - - +
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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