Contacts of the strand formed by residues 438 - 445 (chain A) in PDB entry 4H1J
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 438 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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430A ILE* 4.4 21.4 - - + +
432A GLY 3.7 7.9 - - - +
433A GLU* 4.4 15.7 - - + +
437A GLY* 1.3 76.6 - - - -
439A VAL* 1.3 60.2 + - - +
440A TYR* 3.6 32.8 + - + +
458A THR* 2.7 40.7 + - - +
460A LYS* 6.0 1.0 - - - +
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Residues in contact with VAL 439 (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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430A ILE* 3.6 4.0 - - - +
431A LEU* 2.7 52.2 + - + -
432A GLY* 2.8 16.9 + - - +
433A GLU 4.7 0.7 - - - -
434A GLY* 4.0 23.3 - - - +
437A GLY 4.1 2.5 - - - +
438A GLU* 1.3 77.6 - - - +
440A TYR* 1.3 57.9 + - - +
455A ALA* 4.4 4.3 - - + -
456A VAL 3.4 16.2 - - - +
457A LYS* 4.1 31.9 - - + -
701A 0YH 5.4 7.4 - - + +
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Residues in contact with TYR 440 (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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427A LEU* 4.0 41.1 - - + -
428A ASN 5.7 0.4 - - - -
429A ARG* 3.5 14.8 - - - +
430A ILE* 3.6 30.5 - - + +
431A LEU* 4.3 4.9 - - - -
438A GLU* 3.6 40.7 + - + -
439A VAL* 1.3 76.7 - - - +
441A GLU* 1.3 64.6 + - - +
442A GLY 3.8 0.2 + - - -
455A ALA* 3.3 5.4 - - - -
456A VAL* 2.7 43.0 + - - +
458A THR* 4.2 16.6 - - + -
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Residues in contact with GLU 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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427A LEU* 3.8 2.8 - - - -
428A ASN* 2.9 25.0 + - - -
429A ARG* 2.7 64.2 + - + +
430A ILE 4.8 0.9 - - - +
431A LEU* 3.8 31.7 - - + +
440A TYR* 1.3 74.2 - - - +
442A GLY* 1.3 58.6 + - - +
454A VAL 3.6 4.5 - - - -
504A LEU* 4.1 24.8 - - + +
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Residues in contact with GLY 442 (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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426A VAL 3.2 13.7 - - - -
427A LEU* 4.3 1.6 - - - -
428A ASN* 4.2 5.8 + - - -
440A TYR 3.8 0.6 + - - -
441A GLU* 1.3 74.9 - - - +
443A VAL* 1.3 68.6 + - - +
453A ASN* 3.6 5.7 - - - +
454A VAL* 2.8 40.5 + - - +
456A VAL* 4.8 4.7 - - - -
504A LEU* 5.5 0.7 - - - +
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Residues in contact with VAL 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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424A ASP 3.4 2.4 - - - +
425A VAL* 3.4 2.4 - - - -
426A VAL* 2.9 40.7 + - + +
428A ASN* 3.6 19.3 - - - +
442A GLY* 1.3 78.4 - - - +
444A TYR* 1.3 64.7 + - - +
445A THR* 4.3 4.4 + - - +
451A LYS* 3.9 38.8 - - + -
452A ILE 3.5 5.2 - - - +
453A ASN* 4.0 15.5 - - - +
454A VAL* 3.8 3.3 - - - +
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Residues in contact with TYR 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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420A ILE* 3.8 31.4 - - + +
424A ASP* 3.5 24.6 + - + -
425A VAL* 3.9 19.1 - - + -
443A VAL* 1.3 72.2 - - - +
445A THR* 1.3 76.4 + - - +
446A ASN* 3.9 25.9 - - + +
447A HIS* 4.1 15.4 + - - -
450A GLU 3.5 2.1 - - - +
451A LYS* 3.5 0.7 - - - -
452A ILE* 2.7 62.7 + - + +
454A VAL* 3.8 16.0 - - + +
490A ILE* 3.8 25.8 - - + -
501A ILE* 5.0 1.1 - - + -
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Residues in contact with THR 445 (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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424A ASP* 2.9 40.6 + - - +
443A VAL* 4.3 5.7 + - - +
444A TYR* 1.3 76.8 - - - +
446A ASN* 1.3 65.9 + - - +
449A GLY* 3.8 30.7 - - - +
450A GLU 3.4 4.7 - - - +
451A LYS* 3.9 19.2 - - + +
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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