Contacts of the strand formed by residues 222 - 226 (chain 1) 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 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141 LEU* 3.6 1.0 - - - -
151 HIS* 2.9 36.5 + - - +
171 LEU* 4.5 4.2 - - - +
2141 TYR* 3.5 22.4 - - - -
2201 ILE 3.6 2.4 + - - -
2211 PRO* 1.3 74.8 - - - +
2231 LEU* 1.3 63.9 + - - +
2511 ILE* 4.4 0.4 - - - -
2521 LEU 3.0 14.4 - - - -
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Residues in contact with LEU 223 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121 CYS* 4.3 5.8 - - + -
131 ASP 3.2 9.9 - - - +
141 LEU* 4.0 13.0 - - + -
171 LEU* 4.6 3.1 - - + -
211 PRO* 4.0 17.7 - - + -
2141 TYR* 3.7 4.5 - - - +
2221 GLY* 1.3 74.6 - - - +
2241 ARG* 1.3 61.6 + - - +
2251 VAL* 3.9 1.8 + - + -
2361 ALA* 4.1 23.3 - - + +
2391 PHE* 3.9 24.2 - - + -
2401 ALA* 4.8 2.2 - - + -
2511 ILE* 3.5 26.7 - - + -
2521 LEU 2.9 22.1 + - - +
2531 MET* 3.3 21.8 - - + +
2541 GLU 3.1 21.8 + - - -
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Residues in contact with ARG 224 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101 LYS* 5.9 1.6 - - - +
111 LYS 4.7 1.0 - - - +
121 CYS* 3.5 7.8 - - - -
131 ASP* 2.8 63.9 + - - +
2111 THR 5.3 1.8 + - - -
2121 ASP* 3.8 13.9 + - - +
2141 TYR* 3.5 41.3 + - + -
2231 LEU* 1.3 73.1 - - - +
2251 VAL* 1.3 64.2 + - - +
2541 GLU* 3.2 39.2 + - - +
2561 GLN* 3.5 30.6 + - + +
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Residues in contact with VAL 225 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101 LYS* 6.5 0.7 - - - -
121 CYS* 3.8 15.3 - - - -
2231 LEU* 4.1 5.4 - - + +
2241 ARG* 1.3 77.5 - - - +
2261 ASP* 1.3 78.5 + - - +
2321 CYS* 3.7 26.5 - - + +
2331 VAL* 4.0 4.5 - - - +
2361 ALA* 3.3 33.7 - - + -
2531 MET* 3.9 19.1 - - + -
2541 GLU 2.8 7.3 + - - +
2551 LEU* 3.9 15.5 - - + -
2561 GLN* 2.9 32.8 + - - +
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Residues in contact with ASP 226 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101 LYS* 3.8 35.1 + - + +
2251 VAL* 1.3 80.7 - - - +
2271 GLY* 1.3 63.4 + - - +
2281 MET* 3.0 20.5 + - - +
2291 ASP* 3.4 23.6 + - - +
2321 CYS* 4.0 16.6 - - - +
2331 VAL* 3.1 19.5 - - - +
2561 GLN* 4.3 3.2 - - - +
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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