Contacts of the strand formed by residues 244 - 249 (chain A) in PDB entry 3GRT
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 GLU 244 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189A ARG* 4.2 7.9 + - - -
212A LYS* 3.4 24.6 + - - +
213A THR 3.1 10.3 + - - +
214A SER* 3.0 22.3 + - - +
215A LEU 2.6 31.9 + - - -
242A GLY 3.6 1.0 + - - -
243A VAL* 1.3 70.9 - - - +
245A VAL* 1.3 60.1 + - - +
246A LEU* 3.2 25.1 + - + +
279A ILE* 5.7 1.6 - - - +
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Residues in contact with VAL 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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215A LEU* 3.3 20.2 - - + +
217A ILE* 3.4 37.0 - - + -
222A VAL* 5.1 1.3 - - + -
235A THR* 4.3 16.6 - - + +
238A LEU* 4.4 11.9 - - + -
239A GLU* 3.9 34.6 + - + +
243A VAL* 3.4 6.3 + - + +
244A GLU* 1.3 73.7 - - - +
246A LEU* 1.3 61.6 + - - +
247A LYS* 3.5 24.5 + - + +
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Residues in contact with LEU 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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214A SER* 3.8 21.5 - - - +
215A LEU 2.6 13.3 + - - +
216A MET* 3.6 34.1 - - + -
217A ILE* 2.8 30.0 + - - +
244A GLU* 3.2 34.8 - - + +
245A VAL* 1.3 72.5 - - - +
247A LYS* 1.3 59.5 + - - +
249A SER* 3.8 16.0 - - - +
265A MET* 4.0 17.9 - - + -
279A ILE* 4.7 9.9 - - + -
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Residues in contact with LYS 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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217A ILE* 3.5 1.8 - - + -
219A HIS 2.9 18.2 - - - +
220A ASP* 3.4 28.2 + - + +
235A THR* 4.3 7.8 - - - +
239A GLU* 3.5 27.7 + - - -
245A VAL* 3.5 27.3 + - + +
246A LEU* 1.3 69.2 - - - +
248A PHE* 1.3 78.7 + - + +
249A SER* 2.9 15.5 + - - -
267A THR* 3.5 9.5 - - - +
269A VAL* 4.6 1.4 - - + +
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Residues in contact with PHE 248 (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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217A ILE 3.0 7.1 + - - -
218A ARG* 3.4 19.7 - - - -
219A HIS* 3.0 22.9 + + + -
220A ASP* 3.7 38.1 - - + -
247A LYS* 1.3 80.9 - - + +
249A SER* 1.3 58.5 + - - +
250A GLN* 5.0 2.8 - - - +
266A VAL 3.3 2.1 - - - +
268A ALA* 2.9 46.0 + - - +
269A VAL* 3.9 14.8 - - + +
270A PRO* 3.6 35.0 - - + -
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Residues in contact with SER 249 (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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216A MET* 3.9 11.4 - - - +
217A ILE 3.2 16.2 + - - +
218A ARG* 4.1 2.8 - - - +
246A LEU* 3.8 19.1 - - - +
247A LYS 2.9 12.3 + - - -
248A PHE* 1.3 76.2 - - - +
250A GLN* 1.3 69.0 + - - +
265A MET* 3.6 28.5 - - - +
266A VAL 3.2 4.5 - - - -
267A THR* 2.9 19.8 + - - +
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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