Contacts of the strand formed by residues 344 - 349 (chain A) in PDB entry 4I2D
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 VAL 344 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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303A VAL* 3.7 26.9 - - + -
308A ALA* 4.0 26.0 - - + -
311A VAL* 4.4 7.0 - - + -
330A MET* 3.9 16.8 - - + -
334A PHE* 4.2 5.2 - - + -
343A ASP* 1.3 79.2 - - - +
345A ASP* 1.3 63.9 + - - +
346A PHE* 3.6 29.8 - - + -
431A ILE* 4.0 15.0 - - + -
432A ARG 3.0 4.5 + - - +
433A VAL* 3.2 9.5 - - - +
434A ASP 3.0 21.8 + - - -
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Residues in contact with ASP 345 (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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330A MET* 3.4 9.7 - - - +
331A THR* 2.8 44.3 + - - +
332A GLY* 4.2 1.2 - - - -
334A PHE* 5.7 0.4 - - - -
343A ASP* 2.8 11.8 - - - +
344A VAL* 1.3 72.8 - - - +
346A PHE* 1.3 65.4 + - - +
434A ASP* 3.0 18.2 - - + +
436A VAL* 6.2 0.7 - - + -
450A TRP* 4.5 9.6 - - + -
601A MG 2.7 15.2 - - - -
603A APC 2.7 16.3 + - - +
604A ZN 2.4 35.9 - - - -
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Residues in contact with PHE 346 (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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311A VAL* 3.7 16.8 - - + -
312A SER* 3.5 47.3 - - - -
315A VAL* 3.7 8.5 - - + -
328A VAL* 3.9 26.5 - - + -
329A THR 3.2 4.9 - - - +
330A MET* 3.8 23.8 - - + -
331A THR* 4.3 3.6 - - - -
344A VAL* 3.6 37.7 - - + -
345A ASP* 1.3 74.8 - - - +
347A LEU* 1.3 61.4 + - - +
348A ILE* 4.8 1.6 - - + -
433A VAL* 4.1 1.6 - - + -
434A ASP 3.0 6.5 + - - +
435A LEU* 3.6 29.8 - - + -
436A VAL* 3.0 30.8 + - - +
450A TRP* 6.5 0.2 - - - -
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Residues in contact with LEU 347 (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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327A LEU 3.5 1.7 - - - +
328A VAL* 3.4 3.5 - - - -
329A THR* 2.8 37.9 + - - +
331A THR* 3.9 15.7 - - + +
346A PHE* 1.3 73.0 - - - +
348A ILE* 1.3 61.6 + - - +
349A THR* 5.4 2.9 - - + -
436A VAL* 3.5 25.1 - - + +
438A CYS* 3.7 30.5 - - + -
443A ARG* 3.7 15.9 - - + +
446A ALA* 3.8 11.9 - - + -
447A LEU* 3.5 40.6 - - + +
450A TRP* 5.2 4.7 - - + -
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Residues in contact with ILE 348 (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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315A VAL* 4.5 0.7 - - + -
319A VAL* 3.8 33.9 - - + -
326A ALA* 4.3 6.1 - - + -
327A LEU 3.4 7.4 - - - +
328A VAL* 4.2 16.2 - - + -
346A PHE* 4.8 4.5 - - + +
347A LEU* 1.3 80.3 - - - +
349A THR* 1.3 64.4 - - - +
361A LEU* 3.7 25.1 - - + -
362A LEU* 3.9 27.1 - - + -
435A LEU* 4.0 24.2 - - + -
436A VAL 2.7 12.2 + - - +
437A MET* 3.4 11.1 - - - +
438A CYS 3.1 24.9 + - - -
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Residues in contact with THR 349 (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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326A ALA* 3.3 3.5 - - - -
327A LEU* 2.7 52.9 + - + +
347A LEU* 5.4 4.0 - - + -
348A ILE* 1.3 76.8 - - - +
350A SER* 1.3 61.9 + - - +
437A MET* 4.2 5.6 - - - -
438A CYS* 3.0 29.5 + - - -
439A PRO 3.7 1.2 + - - -
440A TYR* 3.2 24.3 - - + -
443A ARG* 4.0 28.3 - - + -
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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