Contacts of the strand formed by residues 475 - 481 (chain D) in PDB entry 1XFV
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 475 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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365D PRO* 3.9 2.9 - - - +
366D PHE* 2.9 35.4 + - + +
367D ASP 4.5 1.2 + - - -
400D LYS* 2.8 49.0 + - + -
401D ILE 3.3 15.9 - - - +
402D PRO* 4.6 9.6 - - + -
455D TYR* 5.7 0.9 + - - -
472D ARG* 4.2 16.8 + - - -
473D ASN* 2.8 26.5 - - + +
474D ILE* 1.3 76.0 - - - +
476D VAL* 1.3 61.5 + - - +
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Residues in contact with VAL 476 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360D VAL* 4.9 1.8 - - + -
363D TYR* 3.9 23.8 - - + -
364D ILE 3.7 8.5 - - - +
365D PRO* 4.2 4.7 - - + -
366D PHE 4.1 1.1 - - - +
400D LYS* 3.3 5.8 - - - +
401D ILE* 2.9 43.3 + - + +
403D LEU* 3.6 41.7 - - + -
474D ILE* 4.2 4.3 - - + +
475D GLU* 1.3 77.3 - - - +
477D MET* 1.3 65.2 + - - +
487D PRO* 3.9 26.7 - - + -
488D LEU 5.5 0.2 - - - +
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Residues in contact with MET 477 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350D VAL* 4.3 10.8 - - + -
364D ILE* 2.8 36.8 + - + +
365D PRO 4.3 0.7 - - - +
366D PHE* 4.3 16.4 - - - -
387D ASN* 3.6 53.4 - - - +
390D SER* 4.4 0.9 - - - -
391D ILE* 4.3 5.8 - - + -
398D ILE* 3.8 29.6 - - + -
399D GLY 3.6 12.1 - - - +
400D LYS* 4.8 0.7 - - - -
476D VAL* 1.3 76.5 - - - +
478D ALA* 1.3 56.3 + - - +
487D PRO* 3.5 2.4 - - - +
488D LEU* 2.7 38.9 + - + +
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Residues in contact with ALA 478 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398D ILE* 3.6 2.4 - - - +
399D GLY 2.7 41.6 + - - +
401D ILE* 3.6 27.4 - - + -
477D MET* 1.3 78.7 - - - +
479D LYS* 1.3 58.1 + - - +
485D LEU* 4.2 4.3 - - + +
486D LYS 2.7 33.2 - - - +
487D PRO* 3.6 1.8 - - + -
488D LEU* 3.7 9.5 - - - +
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Residues in contact with LYS 479 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344D ALA* 4.2 17.0 - - + -
345D THR 3.8 16.4 - - - +
347D GLY* 4.7 10.3 - - - +
349D ASN* 3.3 23.0 + - - +
397D GLU* 2.8 13.0 - - - +
398D ILE* 3.5 14.3 - - + +
478D ALA* 1.3 74.2 - - - +
480D ASN* 1.3 73.5 + - - +
481D VAL* 3.6 6.5 - - + +
485D LEU* 3.5 4.8 - - - -
486D LYS 3.2 26.0 + - - +
488D LEU* 3.3 25.1 - - + +
571D GLY 5.3 0.9 - - - +
576D ASN* 5.3 6.3 - - - +
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Residues in contact with ASN 480 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396D GLY 3.6 13.1 - - - +
397D GLU* 2.6 47.0 + - + +
479D LYS* 1.3 82.3 + - - +
481D VAL* 1.3 97.7 + - - +
482D GLU 3.5 0.6 - - - +
483D GLY* 3.1 36.7 + - - +
484D VAL 3.6 5.9 - - - +
485D LEU* 4.3 9.0 - - + -
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Residues in contact with VAL 481 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344D ALA* 4.6 5.4 - - + -
479D LYS* 3.6 14.6 - - + +
480D ASN* 1.3 88.8 - - - +
482D GLU* 1.3 75.8 + - + +
484D VAL* 3.0 34.3 + - - +
486D LYS* 3.7 29.1 - - + +
565D LYS* 5.6 1.6 - - - +
570D THR 5.1 1.6 - - - +
571D GLY 3.5 32.5 - - - +
572D GLY* 3.7 11.0 - - - +
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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