Contacts of the strand formed by residues 220 - 225 (chain A) in PDB entry 2YD4
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 ALA 220 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140A PRO* 3.7 27.1 - - + +
141A GLN* 3.5 33.2 - - - +
142A LEU 4.6 1.6 - - - +
153A MET* 4.9 6.9 - - - +
202A GLY 3.8 0.3 - - - +
204A TYR* 2.8 43.8 + - + +
219A PRO* 1.3 75.1 - - - +
221A ASN* 1.3 63.0 + - - +
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Residues in contact with ASN 221 (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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142A LEU* 3.5 13.0 - - + +
143A LYS* 2.9 26.6 + - - +
153A MET* 5.7 0.7 - - - -
202A GLY 3.4 2.9 - - - -
203A LYS* 3.5 26.7 + - - +
219A PRO* 4.3 0.8 - - - +
220A ALA* 1.3 74.0 + - - +
222A LEU* 1.3 59.9 + - - +
223A TYR* 3.2 35.1 + - + +
1234A PEG 3.4 26.2 + - - -
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Residues in contact with LEU 222 (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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143A LYS* 3.3 30.1 - - + -
145A VAL* 4.1 5.8 - - + -
151A ALA* 4.4 7.0 - - + -
153A MET* 4.0 13.5 - - + -
193A ILE* 3.5 31.0 - - + -
196A SER* 5.4 0.9 - - - +
200A ASP* 3.8 15.7 - - + +
201A GLN* 3.3 23.6 - - - +
202A GLY 3.0 9.9 + - - -
204A TYR* 3.7 20.0 - - + -
220A ALA 3.9 0.2 + - - -
221A ASN* 1.3 72.9 - - - +
223A TYR* 1.3 76.6 + - - +
224A VAL* 4.0 15.9 - - + -
1234A PEG 3.4 6.2 - - - +
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Residues in contact with TYR 223 (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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142A LEU* 3.9 29.9 - - + +
143A LYS 2.8 15.6 + - - +
144A VAL* 3.4 14.2 - - + +
145A VAL* 3.0 28.6 + - - +
201A GLN* 3.5 5.2 - - - +
221A ASN* 3.2 41.2 + - + -
222A LEU* 1.3 74.1 - - - +
224A VAL* 1.3 64.8 + - - +
225A ARG* 6.3 0.2 - - + -
1234A PEG 3.7 35.6 - - - -
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Residues in contact with VAL 224 (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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145A VAL* 3.1 11.7 - - + +
147A ARG* 3.6 41.5 - - + +
196A SER* 4.3 5.2 - - - -
197A GLU 3.4 26.0 - - - +
198A GLU* 4.4 15.2 - - + +
201A GLN* 2.8 30.5 + - + +
222A LEU* 4.0 12.1 - - + -
223A TYR* 1.3 77.0 - - - +
225A ARG* 1.3 63.4 + - - +
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Residues in contact with ARG 225 (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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144A VAL* 3.6 26.5 - - + +
145A VAL* 2.9 18.2 + - - +
146A GLU* 3.3 17.8 - - - +
147A ARG* 3.0 27.0 + - - +
223A TYR 4.1 0.2 + - - -
224A VAL* 1.3 77.2 - - - +
226A VAL* 1.3 85.5 + - - +
227A GLY* 4.5 2.0 + - - -
228A THR* 4.3 23.9 - - - +
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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