Contacts of the strand formed by residues 440 - 444 (chain A) in PDB entry 2IVF
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 THR 440 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249A LEU* 3.1 25.1 - - - +
251A PHE* 3.5 36.3 - - + -
435A VAL* 4.0 5.0 + - + -
438A LYS 2.8 17.8 + - - -
439A ARG* 1.3 74.5 - - - +
441A CYS* 1.3 65.1 + - - +
465A MET* 3.7 21.3 - - + +
470A ASN* 2.9 27.8 + - - +
475A GLY 3.4 6.9 - - - +
476A THR* 3.5 16.3 - - - +
477A GLY 4.4 1.6 + - - +
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Residues in contact with CYS 441 (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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239A TYR* 3.5 38.1 - - - -
243A ASN* 3.6 20.9 - - - -
244A LEU* 3.9 14.8 - - + -
247A ALA* 3.7 15.7 - - + +
249A LEU 3.0 4.7 + - - +
250A ILE* 3.1 9.2 - - - +
251A PHE 2.9 22.2 + - - -
440A THR* 1.3 73.6 - - - +
442A SER* 1.3 62.6 + - - +
475A GLY 3.3 14.6 + - - +
476A THR* 3.9 4.3 - - - +
477A GLY 3.7 7.4 - - - -
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Residues in contact with SER 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A TYR* 2.7 25.6 + - - -
250A ILE* 5.3 0.4 - - - -
251A PHE* 3.1 22.3 - - - +
252A MET* 5.3 1.3 - - - -
253A THR* 5.1 0.4 - - - -
441A CYS* 1.3 77.0 - - - +
443A TYR* 1.3 58.2 + - - +
444A ILE* 4.6 1.6 - - - -
461A LEU* 4.3 17.9 - - - +
465A MET* 3.7 26.0 - - - +
477A GLY 2.9 11.5 + - - -
478A ALA* 3.1 25.7 - - - -
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Residues in contact with TYR 443 (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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87A TRP* 3.8 16.8 + - - -
88A PRO* 3.7 22.9 - - + +
225A TYR* 4.5 0.8 + - - -
239A TYR* 3.3 20.6 - + - +
251A PHE 2.7 10.0 + - - -
252A MET* 3.7 22.0 - - + +
253A THR* 2.9 29.0 + - - +
255A SER* 3.3 16.8 + - - -
257A TRP* 3.2 35.2 - + - -
442A SER* 1.3 71.4 - - - +
444A ILE* 1.3 71.4 + - - +
445A GLY* 3.8 10.8 - - - -
446A PHE* 4.4 7.4 - - - -
478A ALA 3.4 0.7 - - - -
479A PHE* 3.8 8.7 - - - -
480A ALA* 3.7 29.0 + - + -
1986A MGD 4.1 8.7 + - - -
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Residues in contact with ILE 444 (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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225A TYR* 2.6 40.5 + - + -
253A THR* 3.4 23.3 - - + +
254A CYS* 4.5 2.0 - - + -
442A SER* 4.6 2.2 - - - -
443A TYR* 1.3 75.3 - - - +
445A GLY* 1.3 55.9 + - - +
448A SER* 3.6 31.2 - - - +
458A GLU* 4.3 13.9 - - + -
461A LEU* 3.8 22.4 - - + -
462A PHE* 3.9 28.7 - - + -
478A ALA* 2.8 24.1 + - + +
479A PHE* 3.7 8.7 - - + +
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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