Contacts of the strand formed by residues 354 - 358 (chain A) in PDB entry 1AX4
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 ALA 354 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197A GLY 4.5 0.3 - - - +
332A VAL* 3.7 14.2 - - - +
350A THR* 4.6 0.7 - - - -
351A GLY* 3.9 15.8 + - - -
353A HIS* 1.3 100.9 + - + +
355A VAL* 1.3 66.2 + - - +
356A PHE* 3.8 26.0 - - + -
414A ARG* 4.0 7.6 - - + -
415A LEU 3.2 14.4 - - - +
416A THR* 3.9 7.2 - - - -
417A ILE* 4.5 1.8 - - - +
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Residues in contact with VAL 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A VAL* 3.4 31.9 - - + +
335A LEU* 4.0 12.8 - - + -
336A GLY* 3.7 15.5 - - - +
339A LEU* 4.0 16.8 - - + -
346A ILE* 3.9 28.5 - - + -
350A THR* 4.0 8.5 - - + -
354A ALA* 1.3 76.3 - - - +
356A PHE* 1.3 64.5 + - - +
357A VAL* 4.2 4.5 - - + -
413A MET 3.6 1.9 - - - +
414A ARG* 3.6 0.7 - - - -
415A LEU* 2.7 47.8 + - + +
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Residues in contact with PHE 356 (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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194A ASN* 4.1 9.9 - - - -
195A SER* 5.1 5.4 - - - -
197A GLY* 3.2 44.9 - - - -
346A ILE* 3.2 5.5 - - - +
347A GLN* 3.0 42.2 + - + +
353A HIS* 4.9 2.7 - + - -
354A ALA* 3.8 16.2 - - + -
355A VAL* 1.3 78.4 - - - +
357A VAL* 1.3 59.5 + - - +
391A ILE* 4.9 10.1 - - + -
412A PHE* 3.8 36.2 - + + -
413A MET 3.3 4.9 - - - -
414A ARG* 3.3 43.5 - - + -
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Residues in contact with VAL 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A LEU* 3.8 28.3 - - + -
344A ILE* 3.8 21.1 - - + -
345A PRO 3.5 4.3 - - - -
346A ILE* 4.1 7.4 - - + -
355A VAL* 4.2 1.3 - - + -
356A PHE* 1.3 74.9 - - - +
358A ASP* 1.3 64.0 + - - +
359A CYS* 3.9 1.8 - - - -
362A LEU* 3.9 18.4 - - + -
412A PHE* 3.1 13.3 - - - -
413A MET* 2.9 56.2 + - + +
415A LEU* 4.1 16.2 - - + -
434A LEU* 4.2 2.7 - - + -
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Residues in contact with ASP 358 (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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157A SER* 4.6 6.2 + - - +
345A PRO* 3.0 18.5 + - + +
346A ILE 6.1 0.4 - - - -
357A VAL* 1.3 71.3 - - - +
359A CYS* 1.3 59.7 + - - +
360A LYS* 3.1 27.9 + - - +
361A LYS* 3.6 38.2 + - + +
362A LEU* 2.9 27.3 - - - +
410A MET* 4.1 19.5 - - - +
411A GLU 3.9 5.8 + - - +
412A PHE* 4.2 13.2 - - + -
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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