Contacts of the strand formed by residues 245 - 250 (chain A) in PDB entry 1XI1
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 GLY 245 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244A GLU* 1.3 75.0 - - - +
246A MET* 1.3 59.6 + - - -
462A LEU 3.0 14.4 - - - -
463A THR* 4.1 0.2 - - - -
464A GLY 3.1 11.8 + - - -
465A THR* 4.4 1.0 - - - +
488A THR* 3.1 8.0 - - - +
489A PHE* 2.8 49.3 + - - -
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Residues in contact with MET 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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245A GLY* 1.3 73.9 - - - +
247A VAL* 1.3 72.0 + - - +
248A PHE* 3.4 30.7 - - + -
451A ARG* 3.2 28.0 - - - +
460A ILE 3.8 0.6 - - - +
461A HIS* 3.5 0.9 - - - +
462A LEU* 2.8 31.0 + - + +
464A GLY 2.9 15.9 - - - +
465A THR* 3.2 30.5 - - - +
466A GLU 3.5 4.3 - - - +
467A ILE* 3.5 17.0 - - + +
485A HIS* 3.3 29.8 - - + +
487A SER 3.4 6.1 - - - -
488A THR* 4.7 1.1 - - + +
489A PHE* 4.1 0.7 - - - -
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Residues in contact with VAL 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A MET* 1.3 82.1 - - - +
248A PHE* 1.3 65.1 + - - +
249A ASP* 3.5 19.5 - - - +
459A SER* 4.5 0.2 - - - -
460A ILE 3.4 2.7 - - - -
461A HIS* 3.5 39.0 - - + +
485A HIS* 3.7 4.0 + - - -
486A GLU* 2.8 30.9 + - + +
487A SER* 3.0 29.0 + - - +
489A PHE* 4.4 6.3 - - + -
502A GLN* 4.0 20.2 - - - +
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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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246A MET* 3.4 41.3 - - + -
247A VAL* 1.3 76.8 - - - +
249A ASP* 1.3 64.7 + - - +
459A SER* 3.0 5.2 - - - -
460A ILE* 2.9 42.9 + - + +
462A LEU* 3.7 29.8 - - + -
467A ILE* 3.9 18.4 - - + -
468A PRO* 4.1 9.0 - - + -
471A ILE* 5.1 6.7 - - + -
475A VAL* 4.2 21.8 - - + -
483A TRP* 3.7 23.8 - - + -
484A ALA 3.4 5.8 - - - +
485A HIS* 3.7 29.4 - - + -
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Residues in contact with ASP 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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247A VAL* 3.5 14.2 + - - +
248A PHE* 1.3 75.8 - - - +
250A VAL* 1.3 64.4 + - - +
251A ASN* 4.1 0.2 - - - +
458A ASP* 3.3 17.5 - - - +
459A SER* 3.1 23.1 - - - -
483A TRP* 4.0 2.7 - - - -
484A ALA* 2.7 40.4 + - + +
486A GLU* 3.1 40.3 - - + +
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Residues in contact with VAL 250 (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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249A ASP* 1.3 75.4 - - - +
251A ASN* 1.3 67.3 + - - +
252A SER 3.1 8.3 + - - -
253A LEU* 3.8 44.2 + - + -
257A GLN* 5.1 3.4 - - - +
440A THR* 4.4 6.7 - - + -
458A ASP* 2.9 24.0 + - + +
481A GLY* 3.8 22.7 - - - +
482A TYR 3.5 4.5 - - - -
483A TRP* 3.4 42.2 - - + -
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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