Contacts of the strand formed by residues 242 - 247 (chain A) in PDB entry 1GPU
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 THR 242 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178A GLY 5.5 0.3 + - - -
180A LEU 3.1 10.8 + - - -
181A ILE* 3.5 3.1 - - + +
182A ALA 2.8 27.2 + - - +
212A TRP* 3.5 9.0 - - - -
213A GLU* 2.8 38.4 + - - +
215A LEU* 3.9 14.6 - - + -
234A ALA* 3.7 28.6 + - + -
237A SER* 3.2 9.5 + - - -
240A LYS 3.5 3.0 + - - -
241A PRO* 1.3 76.0 + - - +
243A LEU* 1.3 72.4 + - - +
244A ILE* 4.3 3.8 - - + -
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Residues in contact with LEU 243 (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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155A LEU* 4.4 8.1 - - + -
160A LEU* 5.4 1.6 - - + -
182A ALA* 3.4 25.4 - - + +
184A TYR* 3.8 25.8 - - + -
203A VAL* 4.1 16.8 - - + +
204A ALA* 5.4 0.2 - - - -
207A TYR* 3.6 45.5 - - + -
212A TRP* 3.7 12.7 - - + -
213A GLU 2.9 9.5 + - - +
214A VAL* 3.3 16.2 - - + +
215A LEU 2.8 25.8 + - - +
242A THR* 1.3 75.0 - - - +
244A ILE* 1.3 66.1 + - - +
245A LYS* 3.9 2.6 + - + +
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Residues in contact with ILE 244 (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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181A ILE* 4.1 13.0 - - + -
182A ALA 2.8 14.7 + - - +
183A ILE* 3.6 24.0 - - + +
184A TYR 2.9 26.6 + - - -
215A LEU* 3.5 12.3 - - + +
217A VAL* 3.9 18.4 - - + -
227A ILE* 6.4 1.6 - - + -
230A ALA* 3.7 46.7 - - + +
231A ILE* 3.9 13.2 - - + +
234A ALA* 4.7 0.4 - - + -
242A THR* 4.3 11.4 - - + -
243A LEU* 1.3 76.7 - - - +
245A LYS* 1.3 63.5 + - - +
246A MET* 3.1 10.3 + - + +
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Residues in contact with LYS 245 (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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184A TYR* 3.9 30.5 - - + -
186A ASP* 2.7 38.1 + - + +
188A LYS* 4.0 6.3 - - - +
203A VAL* 5.3 8.3 - - + +
204A ALA* 4.9 11.0 - - + +
214A VAL* 4.8 5.4 - - + -
215A LEU 2.9 14.9 + - - +
216A TYR* 3.5 30.5 - - + +
217A VAL 3.1 22.8 + - - +
243A LEU* 3.9 4.4 + - + +
244A ILE* 1.3 67.3 - - - +
246A MET* 1.3 58.8 + - - +
247A THR* 3.8 6.7 + - - +
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Residues in contact with MET 246 (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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36A GLY 4.8 0.4 - - - +
37A MET* 4.0 20.6 - - + -
40A ALA* 3.6 33.7 - - + -
183A ILE* 3.9 19.7 - - + -
184A TYR 3.0 12.1 + - - +
185A ASP* 3.8 3.2 - - - +
186A ASP* 2.8 24.6 + - - -
217A VAL* 3.5 16.6 - - + -
220A GLY* 3.5 25.1 - - - +
227A ILE* 4.0 20.6 - - - -
244A ILE* 3.1 10.3 + - + +
245A LYS* 1.3 69.5 - - - +
247A THR* 1.3 61.1 + - - +
248A THR* 3.5 23.8 + - + +
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Residues in contact with THR 247 (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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186A ASP* 2.8 32.2 + - - +
188A LYS* 4.4 9.9 + - + +
217A VAL 3.0 8.8 + - - -
218A GLU* 3.4 22.1 - - - +
219A ASN* 4.2 0.5 - - - -
220A GLY* 2.8 30.8 + - - -
221A ASN* 4.1 0.7 + - - +
245A LYS* 3.8 7.5 + - - -
246A MET* 1.3 70.8 - - - +
248A THR* 1.3 66.9 + - - +
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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