Contacts of the strand formed by residues 418 - 425 (chain A) in PDB entry 6L9F
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 GLN 418 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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291A PHE* 3.5 2.3 - - - -
292A TRP* 2.8 31.5 + - - +
415A HIS* 3.2 32.6 + - + -
416A GLY* 3.4 2.3 + - - +
417A ALA* 1.3 86.5 + - - +
419A HIS* 1.3 64.7 + - - +
502A ACT 3.6 14.6 - - - +
204C GLU* 3.3 28.3 - - + +
205C PRO* 3.8 37.9 - - + +
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Residues in contact with HIS 419 (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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242A HIS 3.4 17.7 + - - -
243A ILE* 4.3 15.5 - - + +
244A SER 5.4 1.3 - - - -
289A VAL* 4.4 3.6 - - + -
290A LYS 3.0 15.0 - - - +
291A PHE* 3.5 18.4 - + + -
292A TRP* 4.2 5.4 - - - -
418A GLN* 1.3 77.0 + - - +
420A HIS* 1.3 70.1 + - - +
421A ILE* 3.8 32.5 - - + +
502A ACT 3.1 32.0 + - + +
205C PRO* 3.7 8.4 - - - +
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Residues in contact with HIS 420 (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 GLU* 6.0 0.2 - - - -
288A LEU 3.9 0.7 - - - +
289A VAL* 3.5 5.2 - - - +
290A LYS* 2.9 33.7 + - + +
292A TRP* 3.5 19.0 - + + -
419A HIS* 1.3 76.3 + - - +
421A ILE* 1.3 63.3 + - - +
422A TYR* 3.4 29.2 - + + +
200C SER* 3.1 33.6 + - - -
203C GLU* 2.7 25.0 + - - +
205C PRO* 3.4 21.8 - - + +
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Residues in contact with ILE 421 (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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211A SER* 5.9 2.2 - - - -
212A ILE* 3.6 45.8 - - + +
243A ILE* 4.7 8.7 - - + -
255A LEU* 3.6 43.1 - - + +
256A GLU 4.4 1.6 + - - +
287A PHE* 4.4 3.6 - - + -
288A LEU 3.6 7.2 - - - +
289A VAL* 4.4 7.2 - - + -
419A HIS* 3.8 27.6 - - + +
420A HIS* 1.3 76.9 - - - +
422A TYR* 1.3 73.2 + - - +
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Residues in contact with TYR 422 (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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255A LEU* 4.9 1.3 - - - -
256A GLU* 3.3 30.7 - - + +
258A VAL* 3.7 29.8 - - + -
287A PHE* 3.2 14.1 - - - +
288A LEU* 2.8 53.9 + - + +
290A LYS* 4.4 4.9 - - + -
420A HIS* 3.4 33.5 - - + +
421A ILE* 1.3 77.6 - - - +
423A ARG* 1.3 63.2 + - - +
198C PRO* 3.6 12.1 - - + -
200C SER* 2.7 30.1 + - - -
201C PHE* 3.3 39.1 + + - -
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Residues in contact with ARG 423 (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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210A ARG 5.5 3.6 - - - +
254A TYR* 3.7 20.6 - - - -
255A LEU* 2.5 48.3 + - + +
256A GLU 2.9 9.8 + - - +
257A THR* 3.1 31.6 - - + +
258A VAL* 2.9 25.6 + - - -
284A ASN* 6.2 5.2 - - - +
286A PHE 4.0 4.7 - - - +
287A PHE* 3.9 25.4 - - + -
422A TYR* 1.3 73.8 - - - +
424A LEU* 1.3 65.2 + - - +
425A VAL* 4.8 6.6 - - + +
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Residues in contact with LEU 424 (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 VAL* 3.4 28.3 - - + +
260A ILE* 3.8 32.1 - - + -
263A ILE* 3.7 30.1 - - + -
274A LEU* 5.3 3.6 - - + -
278A PHE* 3.7 14.0 - - - -
283A SER* 4.2 7.1 - - - +
286A PHE* 3.0 29.1 + - + +
287A PHE 3.6 32.8 - - - +
288A LEU* 4.0 9.4 - - + +
403A CYS* 5.5 1.6 - - - +
405A ALA* 4.6 4.9 - - + -
422A TYR 3.8 0.2 + - - -
423A ARG* 1.3 73.9 - - - +
425A VAL* 1.3 62.7 + - - +
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Residues in contact with VAL 425 (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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257A THR* 3.9 36.1 - - + +
258A VAL 3.1 16.4 + - - +
259A ASP* 3.4 5.2 - - - +
260A ILE* 3.1 24.1 + - - +
278A PHE* 4.1 7.6 - - - -
423A ARG* 4.3 9.6 - - + +
424A LEU* 1.3 80.1 - - - +
426A LYS* 1.3 82.4 + - + +
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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