Contacts of the strand formed by residues 468 - 473 (chain A) in PDB entry 1IVT
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 468 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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466A ASN 5.2 2.0 - - - +
467A TRP* 1.4 80.1 - - - +
469A ILE* 1.3 59.2 + - - +
470A LYS* 5.1 11.1 - - + +
480A THR* 3.9 18.8 + - + +
481A TYR 3.6 6.5 - - - +
482A ARG* 3.6 42.0 + - - +
483A PHE 4.8 0.2 - - - +
530A LEU* 3.2 4.5 - - - +
531A ILE* 2.9 53.0 + - + +
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Residues in contact with ILE 469 (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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452A VAL* 6.4 0.9 - - + -
454A LEU* 4.9 4.0 - - + -
467A TRP* 4.0 10.8 - - + -
468A GLN* 1.3 72.0 - - - +
470A LYS* 1.3 62.5 + - - +
471A ARG* 5.5 1.3 - - + -
480A THR* 3.1 3.6 - - - +
481A TYR* 2.8 46.8 + - + +
483A PHE* 3.5 27.6 - - + -
497A ILE* 4.1 17.9 - - + -
498A TRP* 3.6 32.5 - - + -
528A THR* 5.4 1.6 - - + -
529A ALA 3.9 6.3 - - - +
530A LEU* 3.4 33.9 - - + -
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Residues in contact with LYS 470 (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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468A GLN* 5.1 8.6 - - - +
469A ILE* 1.3 73.6 - - - +
471A ARG* 1.4 65.8 + - - +
478A LEU* 5.7 6.5 - - + -
479A LEU 3.7 4.5 - - - +
480A THR* 3.2 26.5 - - + +
527A ARG 4.5 0.3 - - - +
528A THR* 4.3 1.2 - - - +
529A ALA* 2.9 46.4 + - + +
531A ILE* 3.6 36.2 - - + +
537A GLU* 5.6 2.9 - - - +
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Residues in contact with ARG 471 (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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469A ILE* 5.5 2.0 - - + -
470A LYS* 1.4 77.6 - - - +
472A GLN* 1.4 60.9 + - - +
473A ASN* 3.6 29.8 + - - +
478A LEU* 3.6 6.3 - - - +
479A LEU* 2.9 54.1 + - + +
498A TRP* 3.6 46.8 - - + +
499A ALA* 4.4 15.4 - - - +
514A TRP* 6.5 0.2 - - - -
517A GLN* 3.7 22.6 - - - +
519A THR 3.7 21.0 + - - -
520A TRP* 3.9 21.4 - - - +
526A LEU* 5.0 3.4 - - - -
527A ARG 3.7 6.3 - - - +
528A THR* 3.7 12.3 - - - +
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Residues in contact with GLN 472 (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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471A ARG* 1.4 72.6 - - - +
473A ASN* 1.4 63.9 + - - +
474A GLY 2.8 25.9 + - - +
475A ASP* 4.3 4.9 - - - +
476A ASP 4.7 5.1 + - - -
477A PRO 4.5 3.1 - - - +
478A LEU* 3.7 28.0 - - + +
526A LEU* 4.0 4.0 - - - +
527A ARG* 3.0 70.7 + - + +
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Residues in contact with ASN 473 (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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471A ARG* 3.6 41.7 + - - +
472A GLN* 1.4 79.1 + - - +
474A GLY* 1.4 52.6 + - - +
476A ASP* 2.7 45.6 + - + +
477A PRO* 3.6 24.3 + - + +
479A LEU* 4.4 6.5 - - - +
517A GLN* 5.7 1.2 - - - +
520A TRP* 3.9 7.8 - - - +
522A CYS 5.5 0.9 - - - +
526A LEU* 3.4 29.4 - - + +
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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