Contacts of the strand formed by residues 308 - 315 (chain A) in PDB entry 6FD3
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 308 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299A THR* 3.8 20.5 + - - +
300A ALA 3.4 10.5 - - - +
301A LEU* 3.8 16.2 - - + +
306A GLY 3.4 2.8 + - - +
307A GLN* 1.3 84.6 + - - +
309A VAL* 1.3 64.7 + - - +
359A TYR* 3.5 43.8 + - + +
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Residues in contact with VAL 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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283A TYR* 3.8 33.0 - - + -
299A THR* 3.3 8.0 - - - -
300A ALA 2.9 37.5 + - - +
302A ASP* 5.1 3.1 - - + +
307A GLN* 3.8 24.7 - - + +
308A GLU* 1.3 79.2 - - - +
310A ALA* 1.3 60.5 + - - +
311A ILE* 4.0 9.9 - - + -
344A LEU* 3.8 22.4 - - + -
356A VAL* 3.9 12.8 - - + -
357A MET 3.6 9.0 - - - +
358A GLU* 5.5 0.4 - - - -
359A TYR* 3.7 8.5 - - - +
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Residues in contact with ALA 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A ILE* 4.7 0.9 - - + -
297A VAL* 4.2 9.0 - - + -
298A TYR 3.2 9.4 - - - +
299A THR* 4.6 0.2 - - - +
309A VAL* 1.3 72.5 - - - +
311A ILE* 1.3 64.0 + - - +
312A LYS 4.2 0.2 - - - -
355A VAL 3.8 0.2 - - - +
356A VAL* 3.5 3.5 - - - +
357A MET* 2.9 37.7 + - + +
358A GLU 3.8 5.2 - - - +
359A TYR* 3.8 10.2 - - + +
603A ADP 3.4 37.2 - - + +
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Residues in contact with ILE 311 (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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283A TYR* 3.6 42.4 - - + -
286A PHE* 3.8 23.3 - - + -
296A THR 3.6 2.1 - - - +
297A VAL* 3.3 4.2 - - - -
298A TYR* 2.8 41.7 + - + +
300A ALA* 3.9 8.7 - - + -
309A VAL* 4.0 10.8 - - + -
310A ALA* 1.3 79.6 - - - +
312A LYS* 1.3 62.2 + - - +
313A GLN* 4.2 6.5 - - + +
354A TRP* 3.5 36.8 - - + -
355A VAL 3.4 8.7 - - - +
356A VAL* 4.3 10.5 - - + -
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Residues in contact with LYS 312 (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 SER* 4.5 1.5 - - - -
295A GLY* 4.3 5.8 - - - +
296A THR 3.5 3.6 - - - -
297A VAL* 4.0 13.2 - - + -
311A ILE* 1.3 71.6 - - - +
313A GLN* 1.3 62.5 + - - +
314A MET* 3.9 30.4 - - + +
328A GLU* 2.8 28.8 + - - +
353A LEU 3.5 1.7 - - - +
354A TRP* 3.1 5.9 - - - -
355A VAL* 2.8 40.0 + - + +
357A MET* 3.8 22.0 - - + +
420A ASP* 3.2 8.5 + - - +
422A GLY* 5.4 0.2 - - - -
603A ADP 2.8 60.6 + - - +
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Residues in contact with GLN 313 (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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286A PHE* 3.6 14.0 - - - -
295A GLY* 3.2 2.6 - - - -
296A THR* 2.8 36.2 + - - +
298A TYR* 3.3 38.7 + - + -
311A ILE* 4.2 4.2 - - + +
312A LYS* 1.3 77.0 - - - +
314A MET* 1.3 59.9 + - - +
352A GLU* 5.4 3.6 - - - +
353A LEU 3.5 4.5 - - - -
354A TRP* 3.0 56.3 - - + +
604A EDO 3.4 8.4 - - - -
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Residues in contact with MET 314 (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 SER* 3.4 24.5 - - - +
295A GLY* 3.8 11.0 - - - -
312A LYS* 3.9 23.8 - - + +
313A GLN* 1.3 74.5 - - - +
315A ASN* 1.3 60.6 + - - +
316A LEU* 3.7 2.0 + - + +
319A GLN* 3.9 9.4 - - - +
325A ILE* 4.0 17.7 - - + -
328A GLU* 3.7 21.8 - - - +
352A GLU* 3.3 7.6 + - - -
353A LEU* 2.7 72.9 + - + +
354A TRP* 5.0 0.2 - - - -
355A VAL* 3.8 21.8 - - + -
604A EDO 3.7 3.8 - - - -
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Residues in contact with ASN 315 (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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314A MET* 1.3 70.6 - - - +
316A LEU* 1.3 64.4 + - - +
317A GLN* 3.3 13.2 + - - +
318A GLN* 3.2 33.1 + - + +
319A GLN* 2.7 22.6 + - - -
351A ASP* 3.6 8.3 - - - +
352A GLU* 3.4 29.1 + - - +
604A EDO 2.9 19.0 + - - +
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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