Contacts of the strand formed by residues 432 - 436 (chain A) in PDB entry 5XOU
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 SER 432 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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406A VAL 3.2 10.3 - - - -
408A VAL* 4.2 11.0 - - - -
421A LEU* 5.9 1.4 - - - +
422A LYS* 3.0 47.5 + - - +
425A LEU* 3.8 24.2 - - - -
430A LEU 3.7 1.0 + - - -
431A PRO* 1.3 75.3 - - - +
433A GLN* 1.3 60.9 + - - +
434A ILE* 5.2 1.2 - - - +
454A LEU* 5.2 0.4 - - - -
457A LYS* 3.0 22.7 - - - +
683A PHE* 4.8 1.9 + - - +
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Residues in contact with GLN 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A VAL 2.8 6.7 + - - -
407A LEU* 3.6 8.3 - - + +
408A VAL* 2.8 26.3 + - - +
432A SER* 1.3 73.5 - - - +
434A ILE* 1.3 77.1 + - - +
450A ALA* 3.3 33.0 - - + +
453A GLY* 3.6 12.7 - - - -
454A LEU* 3.8 25.3 - - + +
457A LYS* 3.3 20.7 - - + -
685A VAL* 4.0 1.9 - - - +
1C T 2.8 35.2 + - - -
2C G 4.0 15.1 + - - -
3C A 5.0 1.0 + - - -
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Residues in contact with ILE 434 (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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408A VAL* 3.6 19.7 - - + -
410A THR* 3.7 24.0 - - + -
413A MET* 4.3 17.3 - - - -
418A ARG* 3.8 21.5 - - + -
421A LEU* 5.1 4.3 - - + -
422A LYS* 3.6 28.9 - - + -
432A SER* 5.2 1.3 - - - +
433A GLN* 1.3 97.1 + - - +
435A LEU* 1.3 63.0 + - - +
436A ASN* 3.8 5.4 - - - +
1C T 2.8 55.8 + - + +
2C G 3.6 2.8 - - - +
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Residues in contact with LEU 435 (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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361A LEU* 4.2 12.8 - - + -
407A LEU* 4.3 11.0 - - + -
408A VAL 2.9 18.6 + - - +
409A LEU* 3.5 23.3 - - + +
410A THR 3.4 10.4 + - - -
433A GLN 3.9 0.2 + - - -
434A ILE* 1.3 76.2 - - - +
436A ASN* 1.3 69.0 + - - +
437A VAL 3.5 0.3 + - - -
439A LEU* 3.6 30.1 - - + -
446A ARG* 3.9 12.1 - - + +
447A TRP* 4.0 23.6 - - + -
450A ALA* 3.6 27.1 - - + -
451A LEU* 5.2 0.4 - - + -
2C G 3.6 21.1 - - - +
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Residues in contact with ASN 436 (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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410A THR* 3.1 18.7 - - - +
411A PRO 3.7 1.6 - - - +
412A PRO* 3.5 30.4 - - + +
434A ILE* 3.8 2.8 - - - +
435A LEU* 1.3 75.7 - - - +
437A VAL* 1.3 65.9 + - - +
438A PRO 3.5 0.4 - - - +
439A LEU* 4.0 6.8 - - - +
446A ARG* 2.8 27.7 + - - +
1C T 3.4 44.2 + - - +
2C G 2.7 21.5 + - - +
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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