Contacts of the strand formed by residues 303 - 310 (chain A) in PDB entry 2GTI
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 ILE 303 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301A SER* 3.0 16.8 + - - -
302A SER* 1.3 96.2 - - - +
304A HIS* 1.3 72.3 + - - +
305A SER* 6.1 0.4 - - - -
321A THR* 4.2 8.5 - - + -
322A VAL 3.7 4.3 - - - +
323A ILE* 3.8 24.0 - - + -
350A VAL* 5.2 0.2 - - + -
355A PHE* 3.8 36.4 - - + -
366A VAL* 3.4 41.1 - - + -
367A MSE 4.5 4.7 - - - +
368A THR* 5.9 0.9 - - - -
369A PHE 6.1 0.7 - - - +
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Residues in contact with HIS 304 (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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295A GLU* 2.9 27.6 + - - -
299A TYR 4.1 6.0 + - - -
300A ASP* 4.8 3.6 - - - -
301A SER* 3.0 47.2 + - - -
302A SER 4.6 2.4 + - - -
303A ILE* 1.3 77.0 - - - +
305A SER* 1.3 60.7 + - - +
306A TYR* 3.4 35.7 + - + -
320A CYS 3.7 0.4 - - - +
321A THR* 3.1 5.5 - - - -
322A VAL* 2.8 44.1 + - + +
323A ILE* 5.8 0.4 - - - -
324A ASP 6.1 0.2 + - - -
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Residues in contact with SER 305 (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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294A GLN 4.4 1.7 - - - +
295A GLU* 4.3 14.7 + - - +
296A PHE* 4.8 7.8 + - - -
303A ILE 4.3 0.2 + - - -
304A HIS* 1.3 73.7 - - - +
306A TYR* 1.3 65.7 + - - +
319A VAL* 3.2 31.5 - - - +
320A CYS 3.9 2.9 - - - -
321A THR* 4.4 8.6 - - - +
368A THR* 5.2 8.3 - - - +
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Residues in contact with TYR 306 (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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279A LEU* 5.6 5.5 - - + +
282A LEU* 4.7 7.0 - - + -
293A ILE* 3.2 41.3 - - + -
294A GLN 3.5 1.6 - - - -
295A GLU* 3.5 37.1 + - + -
296A PHE* 5.2 1.8 - - - -
304A HIS* 3.4 33.1 + - + -
305A SER* 1.3 80.8 + - - +
307A LEU* 1.3 60.5 - - - +
308A ILE* 3.6 12.7 + - + -
318A SER 2.9 8.9 - - - +
319A VAL* 3.5 0.2 - - - -
320A CYS* 2.8 38.6 + - - +
322A VAL* 4.0 33.4 - - + +
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Residues in contact with LEU 307 (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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292A VAL 3.8 2.6 - - - +
293A ILE* 3.8 0.3 - - - -
294A GLN* 3.0 63.3 + - + +
296A PHE* 3.8 27.1 - - + -
306A TYR* 1.3 70.5 - - - +
308A ILE* 1.3 63.4 + - - +
309A THR* 5.0 5.5 + - - +
316A SER* 5.3 3.6 - - - +
317A LYS 3.2 19.1 - - - +
318A SER* 3.3 24.7 - - - +
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Residues in contact with ILE 308 (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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273A ILE* 3.9 18.8 - - + -
276A LEU* 4.4 9.6 - - + -
282A LEU* 4.2 15.3 - - + -
291A LEU* 3.9 19.7 - - + -
292A VAL 3.7 2.5 - - - +
293A ILE* 3.5 31.4 - - + -
306A TYR* 3.6 16.4 - - + -
307A LEU* 1.3 72.5 - - - +
309A THR* 1.3 66.0 + - - +
316A SER* 3.0 8.3 - - - -
317A LYS* 3.0 34.0 + - + +
320A CYS* 3.5 36.1 - - + -
322A VAL* 4.3 3.4 - - + -
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Residues in contact with THR 309 (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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290A ASN 3.8 0.2 - - - +
291A LEU* 3.6 6.1 - - - -
292A VAL* 3.0 47.1 + - + +
294A GLN* 4.9 10.4 + - - -
307A LEU* 5.0 4.7 + - - +
308A ILE* 1.3 75.9 + - - +
310A ASP* 1.3 69.6 + - - +
311A GLU* 3.7 3.4 + - - +
314A GLY* 5.5 4.5 - - - -
315A SER 3.6 9.0 - - - +
316A SER* 3.9 9.7 - - - -
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Residues in contact with ASP 310 (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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268A PHE* 3.6 17.5 - - + -
273A ILE* 4.4 2.4 - - + +
285A ARG* 2.8 41.6 + - - -
289A SER* 2.8 12.9 + - - -
291A LEU* 3.4 20.8 - - + +
308A ILE 4.3 0.4 - - - -
309A THR* 1.3 73.4 - - - +
311A GLU* 1.3 57.5 + - - +
313A SER* 2.7 35.0 + - - +
314A GLY* 2.8 31.7 + - - -
315A SER 2.9 11.6 + - - +
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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