Contacts of the strand formed by residues 391 - 395 (chain A) in PDB entry 4ZGA
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 GLY 391 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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385A LEU* 4.0 7.6 - - - -
386A VAL 3.3 4.9 - - - -
387A PRO* 5.1 0.4 - - - -
390A LEU* 1.3 75.7 - - - +
392A ARG* 1.3 71.4 + - - +
445A HIS* 3.1 15.8 + - - -
446A LEU* 3.2 41.9 + - - +
448A VAL* 4.5 0.6 - - - +
454A VAL* 5.7 2.0 - - - -
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Residues in contact with ARG 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A VAL* 4.0 9.8 + - - +
230A GLY* 4.2 5.1 - - - -
232A SER 2.6 32.7 + - - -
233A MET* 4.0 11.7 - - - +
384A THR 3.3 1.7 - - - +
385A LEU* 3.2 5.7 - - - +
386A VAL* 2.7 69.3 + - + +
390A LEU* 3.9 17.9 - - + +
391A GLY* 1.3 79.7 - - - +
393A ILE* 1.3 61.8 + - - +
394A ARG* 5.7 1.1 + - - +
435A TYR* 3.5 26.7 + - - -
440A ARG 4.5 3.9 + - - -
441A ILE* 5.2 0.9 - - - +
442A GLU* 3.1 37.1 + - + +
444A ILE 3.8 7.2 - - - +
445A HIS* 3.6 19.3 - - + +
446A LEU* 5.7 0.2 - - - -
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Residues in contact with ILE 393 (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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373A LEU* 3.9 24.5 - - + -
383A ILE* 4.1 21.5 - - + -
384A THR 3.3 6.7 - - - +
385A LEU* 3.8 16.6 - - + -
392A ARG* 1.3 78.3 - - - +
394A ARG* 1.3 73.5 + - - +
408A ILE* 4.5 8.7 - - + -
412A LEU* 4.4 17.7 - - + -
442A GLU* 3.3 19.4 - - - +
444A ILE* 3.4 55.3 + - + +
446A LEU* 4.5 10.3 - - + -
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Residues in contact with ARG 394 (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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233A MET* 5.6 1.0 - - - +
234A TYR* 3.9 47.1 - - - +
241A THR* 5.7 1.8 - - - +
383A ILE* 3.6 8.8 - - - +
384A THR* 3.0 59.8 + - - +
386A VAL* 4.2 18.4 - - - +
392A ARG 5.7 0.8 + - - -
393A ILE* 1.3 81.3 - - - +
395A SER* 1.3 72.2 + - - +
442A GLU* 2.6 38.2 + - + -
444A ILE* 5.4 2.7 - - - -
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Residues in contact with SER 395 (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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382A ASP 4.2 6.1 + - - -
383A ILE* 5.0 2.9 - - - +
384A THR* 4.0 1.7 + - - -
394A ARG* 1.3 91.0 + - - +
396A LYS* 1.3 66.0 + - - +
397A PHE* 3.8 16.3 + - - +
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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