Contacts of the strand formed by residues 221 - 225 (chain 3) in PDB entry 3EPD
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 221 (chain 3).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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443 MET* 4.5 8.3 - - - -
1103 TRP* 3.5 0.5 - - - -
1113 ALA* 2.9 32.9 + - - +
1763 TYR* 2.8 28.8 + - - -
2193 ASP 3.9 2.5 + - - -
2203 PHE* 1.3 78.3 - - - +
2223 VAL* 1.3 70.1 + - - +
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Residues in contact with VAL 222 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433 MET* 6.2 0.9 - - + -
443 MET* 4.0 23.1 - - + +
1033 VAL* 5.3 2.2 - - + -
1043 LEU* 3.4 34.3 - - + -
1073 TYR* 3.6 44.2 - - + -
1093 HIS 3.3 14.6 - - - +
1103 TRP* 4.3 2.2 - - + -
1763 TYR* 4.3 5.1 + - - -
2203 PHE* 4.2 1.8 - - + -
2213 SER* 1.3 81.9 - - - +
2233 ARG* 1.3 66.2 + - - +
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Residues in contact with ARG 223 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1981 TYR 5.4 3.6 + - - -
1991 VAL* 3.9 5.9 + - - -
2001 GLY 2.8 34.0 + - - -
2011 LEU* 3.6 9.9 - - - +
1073 TYR* 3.7 9.1 - - - +
1083 THR 3.2 6.4 + - - -
1093 HIS* 2.9 61.6 + - + +
1753 THR* 4.9 2.2 + - - -
1763 TYR* 3.3 47.5 - - + +
2223 VAL* 1.3 78.1 - - - +
2243 LEU* 1.3 62.1 + - + +
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Residues in contact with LEU 224 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1591 TYR* 4.1 34.8 - - + +
1611 PRO* 4.1 4.5 - - + -
1621 PRO* 6.1 0.2 - - + -
1991 VAL* 4.8 20.2 - - + -
10001 SPH 6.3 0.4 - - + -
1073 TYR* 3.3 1.8 - - - -
1083 THR* 2.8 55.0 + - + +
1093 HIS* 4.0 24.9 - - + +
2233 ARG* 1.3 75.3 - - + +
2253 LEU* 1.3 75.8 + - - +
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Residues in contact with LEU 225 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1611 PRO* 4.2 3.1 - - - +
1781 SER 5.4 0.9 - - - +
1791 SER* 3.9 39.3 - - - +
1801 ASN* 4.7 1.9 - - - -
1811 PRO* 4.9 3.1 - - - +
1063 TYR* 3.3 25.1 - - + +
1073 TYR* 3.8 31.8 - - + +
2243 LEU* 1.3 85.5 - - - +
2263 ARG* 1.3 58.9 + - - +
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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