Contacts of the strand formed by residues 475 - 481 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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365C PRO* 3.9 2.8 - - - +
366C PHE* 2.9 37.0 + - + +
367C ASP 4.5 0.7 + - - -
400C LYS* 2.8 48.1 + - + -
401C ILE 3.3 15.5 - - - +
402C PRO* 4.2 9.9 - - + -
455C TYR* 5.7 0.7 + - - -
472C ARG* 4.1 16.3 + - - -
473C ASN* 2.8 27.6 - - + +
474C ILE* 1.3 76.3 - - - +
476C VAL* 1.3 61.0 + - - +
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Residues in contact with VAL 476 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360C VAL* 4.9 1.3 - - + -
363C TYR* 3.8 25.1 - - + -
364C ILE 3.7 7.4 - - - +
365C PRO* 4.2 4.5 - - + -
366C PHE 4.1 1.6 - - - +
400C LYS* 3.3 6.3 - - - +
401C ILE* 2.9 41.8 + - + +
402C PRO 4.9 0.2 - - - +
403C LEU* 3.6 41.7 - - + -
474C ILE* 4.2 4.3 - - + +
475C GLU* 1.3 78.3 - - - +
477C MET* 1.3 63.5 + - - +
487C PRO* 3.9 27.6 - - + -
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Residues in contact with MET 477 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350C VAL* 4.3 11.2 - - + -
364C ILE* 2.8 38.2 + - + +
365C PRO 4.3 1.1 - - - +
366C PHE* 4.3 16.4 - - - -
387C ASN* 3.6 52.5 - - - +
390C SER* 4.3 0.7 - - - -
391C ILE* 4.3 7.2 - - + -
398C ILE* 3.8 28.5 - - + -
399C GLY 3.6 11.4 - - - +
400C LYS* 4.8 0.7 - - - -
476C VAL* 1.3 75.3 - - - +
478C ALA* 1.3 56.6 + - - +
487C PRO* 3.5 2.4 - - - +
488C LEU* 2.7 39.5 + - + +
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Residues in contact with ALA 478 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398C ILE* 3.6 2.6 - - - +
399C GLY 2.7 41.5 + - - +
401C ILE* 3.6 27.1 - - + -
477C MET* 1.3 79.1 - - - +
479C LYS* 1.3 58.8 + - - +
485C LEU* 4.2 3.4 - - + +
486C LYS 2.7 33.4 - - - +
487C PRO* 3.6 1.8 - - + -
488C LEU* 3.7 9.8 - - - +
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Residues in contact with LYS 479 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344C ALA* 4.2 16.2 - - + -
345C THR 3.8 16.6 - - - +
347C GLY* 4.7 9.6 - - - +
349C ASN* 3.3 23.2 + - - +
397C GLU* 2.8 12.6 - - - +
398C ILE* 3.5 14.5 - - + +
478C ALA* 1.3 72.5 - - - +
480C ASN* 1.3 73.1 + - - +
481C VAL* 3.6 6.2 - - + +
485C LEU* 3.5 4.9 - - - -
486C LYS 3.2 26.1 + - - +
488C LEU* 3.3 25.1 - - + +
571C GLY 5.3 0.4 - - - +
576C ASN* 5.3 6.5 - - - +
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Residues in contact with ASN 480 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396C GLY 3.7 12.6 - - - +
397C GLU* 2.6 47.4 + - + +
479C LYS* 1.3 83.5 + - - +
481C VAL* 1.3 97.2 + - - +
482C GLU 3.5 1.2 - - - +
483C GLY* 3.1 37.0 + - - +
484C VAL 3.6 5.9 - - - +
485C LEU* 4.3 8.3 - - + -
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Residues in contact with VAL 481 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344C ALA* 4.6 5.6 - - + -
479C LYS* 3.6 14.6 - - + +
480C ASN* 1.3 89.1 - - - +
482C GLU* 1.3 76.4 + - + +
484C VAL* 3.0 32.9 + - - +
486C LYS* 3.7 30.4 - - + +
565C LYS* 5.6 0.9 - - - +
570C THR 5.1 1.6 - - - +
571C GLY* 3.5 31.9 - - - +
572C GLY* 3.7 11.4 - - - +
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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