Contacts of the strand formed by residues 222 - 226 (chain 5) in PDB entry 3EXG
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 GLY 222 (chain 5).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145 LEU* 3.6 1.2 - - - -
155 HIS* 2.8 36.4 + - - +
175 LEU* 4.0 4.2 - - - +
2145 TYR* 3.4 23.5 + - - -
2205 ILE 3.6 1.4 + - - -
2215 PRO* 1.3 75.4 - - - +
2235 LEU* 1.3 65.5 + - - +
2525 LEU* 3.1 13.0 - - - -
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Residues in contact with LEU 223 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125 CYS* 3.9 14.1 - - + -
135 ASP 3.1 12.1 - - - +
145 LEU* 4.5 5.8 - - + -
175 LEU* 4.5 4.5 - - + -
215 PRO* 3.8 31.6 - - + -
2145 TYR* 3.6 6.3 - - - +
2225 GLY* 1.3 75.4 - - - +
2245 ARG* 1.3 60.1 + - - +
2255 VAL* 4.4 2.0 - - + -
2365 ALA* 4.5 11.7 - - + +
2395 PHE* 4.1 14.4 - - + -
2405 ALA* 5.2 1.3 - - + -
2515 ILE* 3.5 25.4 - - + -
2525 LEU 3.1 15.6 + - - +
2535 MET* 3.3 23.6 - - + +
2545 GLU 3.0 22.9 + - - -
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Residues in contact with ARG 224 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105 LYS* 5.9 1.6 - - - +
125 CYS* 3.2 28.9 - - - +
135 ASP* 3.0 39.2 + - + +
2115 THR 4.2 4.4 + - - -
2125 ASP* 3.0 26.9 + - - -
2145 TYR* 3.6 31.7 + - + -
2235 LEU* 1.3 73.3 - - - +
2255 VAL* 1.3 62.4 + - - +
2545 GLU* 3.4 30.3 + - - +
2565 GLN* 3.4 39.2 + - + +
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Residues in contact with VAL 225 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105 LYS* 5.9 1.8 - - - -
125 CYS* 3.8 19.1 - - - -
2235 LEU* 4.4 3.8 - - + -
2245 ARG* 1.3 81.9 - - - +
2265 ASP* 1.3 71.4 + - - +
2275 GLY 4.3 1.1 - - - +
2325 CYS* 4.4 6.7 - - + -
2335 VAL* 4.4 19.5 - - + -
2365 ALA* 3.8 19.1 - - + -
2535 MET* 4.1 16.4 - - + -
2545 GLU 2.9 12.6 + - - +
2555 LEU* 4.0 20.0 - - + -
2565 GLN* 3.1 34.5 + - - +
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Residues in contact with ASP 226 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105 LYS* 4.6 32.8 + - + +
2255 VAL* 1.3 75.2 - - - +
2275 GLY* 1.3 57.7 + - - +
2285 MET* 3.4 20.8 + - - +
2295 ASP* 3.1 47.6 + - - +
2325 CYS* 3.5 22.2 - - - +
2335 VAL* 4.0 0.5 - - - +
2565 GLN* 4.5 5.3 - - - +
2905 LEU* 5.8 1.4 - - - +
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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