Contacts of the strand formed by residues 263 - 268 (chain A) in PDB entry 6FEQ
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 ARG 263 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65A SER* 3.4 16.2 - - - -
66A ASN* 2.7 35.4 + - - +
67A ILE* 5.1 0.9 - - - -
259A LEU* 3.7 7.8 - - - +
260A ALA 3.2 28.1 + - - +
261A SER 4.2 6.7 - - - +
262A GLY* 1.3 85.8 - - - +
264A LEU* 1.3 69.5 + - - +
265A MET* 3.4 11.6 + - + +
329A ILE* 4.5 17.0 - - + -
330A GLU* 5.8 7.4 - - + +
333A ALA* 3.8 29.2 - - + +
334A GLU* 5.4 2.8 - - - +
337A VAL* 4.9 13.1 - - - +
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Residues in contact with LEU 264 (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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66A ASN* 4.1 13.2 + - - +
67A ILE* 3.9 23.5 - - + +
68A ASN* 3.5 40.4 - - + +
257A THR* 3.7 19.5 - - + -
258A LEU 4.4 0.2 - - - +
259A LEU* 3.7 8.1 - - + +
263A ARG* 1.3 78.4 + - - +
265A MET* 1.3 59.8 + - - +
266A PHE 3.3 25.4 - - - +
267A HIS* 4.3 3.1 - - + -
333A ALA* 4.6 9.5 - - - +
336A TYR* 3.7 37.3 - - + +
342A TYR* 5.1 4.3 - - + -
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Residues in contact with MET 265 (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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258A LEU* 2.9 25.5 + - + +
259A LEU 4.8 0.7 - - - -
260A ALA* 3.7 32.3 - - - +
263A ARG* 3.5 18.4 - - + +
264A LEU* 1.3 76.3 - - - +
266A PHE* 1.3 63.5 + - - +
276A TYR* 5.1 0.5 - - - -
277A PHE* 4.8 11.4 - - + -
298A ILE* 3.7 24.7 - - + -
329A ILE* 4.6 17.7 - - + +
332A LEU* 3.7 38.6 - - + +
333A ALA* 5.3 5.8 - - + +
336A TYR* 3.4 25.0 - - - +
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Residues in contact with PHE 266 (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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256A LEU* 3.9 16.8 - - + -
257A THR* 3.3 4.0 - - - -
258A LEU* 3.0 41.0 + - + -
264A LEU* 3.3 8.3 - - - +
265A MET* 1.3 80.4 - - - +
267A HIS* 1.3 81.9 + - - +
268A GLY* 3.6 19.5 - - - -
269A PRO 3.7 14.1 - - - -
272A GLU 3.8 10.5 - - - -
273A ALA* 3.6 34.5 - - + -
276A TYR* 4.1 23.8 - + + -
277A PHE* 4.7 6.3 - + + -
336A TYR* 3.7 13.5 - + - -
341A PHE* 3.6 28.5 - + - -
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Residues in contact with HIS 267 (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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39A PHE* 4.7 7.2 - + - -
68A ASN 3.9 12.9 + - - +
69A GLY* 3.4 24.1 - - - -
70A ILE* 3.1 33.4 + - - +
71A MET* 5.0 3.8 - - + -
255A SER* 4.3 14.5 + - - -
256A LEU 3.3 5.4 + - - -
257A THR* 2.7 26.3 + - - +
264A LEU* 4.3 4.7 - - + -
266A PHE* 1.3 86.5 - - - +
268A GLY* 1.3 61.1 + - - +
336A TYR* 3.2 23.8 + - - +
341A PHE* 4.1 17.2 - - - +
345A THR* 3.8 17.5 + - - -
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Residues in contact with GLY 268 (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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72A LYS* 6.2 0.7 - - - -
255A SER* 3.2 8.7 + - - -
256A LEU* 2.6 39.5 + - - +
266A PHE* 3.6 7.5 - - - -
267A HIS* 1.3 83.0 + - - +
269A PRO* 1.3 70.5 - - - +
341A PHE* 5.8 1.3 - - - -
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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