Contacts of the strand formed by residues 425 - 433 (chain A) in PDB entry 5IXM
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 MET 425 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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417A GLU* 4.1 6.7 - - - +
418A TYR 3.4 13.9 - - - +
419A ARG* 4.4 10.3 - - + +
423A ASP 5.5 0.4 - - - -
424A ARG* 1.3 75.5 - - - +
426A ILE* 1.3 78.2 + - - +
427A GLN* 3.7 8.7 - - + +
460A THR* 3.1 42.8 - - + +
461A ALA* 3.2 8.5 - - - +
462A SER* 2.9 39.6 + - - +
463A TRP* 3.7 4.2 - - - -
545A LEU* 4.9 9.0 - - - -
552A TYR* 3.3 45.5 - - + +
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Residues in contact with ILE 426 (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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416A MET* 5.0 13.2 - - + +
417A GLU* 3.4 3.8 - - - +
418A TYR* 2.8 46.9 + - + +
425A MET* 1.3 81.3 - - - +
427A GLN* 1.3 68.6 + - - +
428A LEU* 5.7 5.4 - - + -
459A THR* 6.5 1.1 - - + -
460A THR 3.5 7.9 - - - +
461A ALA* 4.6 9.2 - - + -
463A TRP* 3.6 31.4 - - + -
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Residues in contact with GLN 427 (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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415A ILE* 3.7 27.8 - - + +
416A MET 3.4 11.7 - - - +
417A GLU* 2.6 33.7 + - + +
425A MET* 3.8 12.1 - - + -
426A ILE* 1.3 81.1 - - - +
428A LEU* 1.3 63.7 + - - +
429A ASN* 5.0 4.7 - - + +
458A GLY 3.7 0.9 - - - +
459A THR* 3.2 7.3 - - - -
460A THR* 2.9 41.5 + - - +
476A TYR* 4.5 12.6 + - - -
552A TYR* 3.4 24.3 - - - -
553A GLN 3.5 14.2 + - - +
555A ALA 3.9 1.0 - - - +
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Residues in contact with LEU 428 (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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415A ILE* 3.2 3.3 - - - +
416A MET* 2.9 65.0 + - + +
426A ILE* 5.7 4.9 - - + -
427A GLN* 1.3 73.7 - - - +
429A ASN* 1.3 64.6 + - - +
457A VAL* 5.3 9.2 - - + -
458A GLY 3.4 6.5 - - - +
459A THR* 3.6 26.7 - - + -
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Residues in contact with ASN 429 (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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414A ALA 3.2 12.6 - - - +
415A ILE* 3.7 19.5 - - + +
427A GLN* 5.0 4.5 - - + +
428A LEU* 1.3 80.2 - - - +
430A TYR* 1.3 64.2 + - - +
431A ARG* 3.8 24.6 - - + +
456A GLN* 4.5 5.1 + - - +
457A VAL* 3.5 7.1 - - - +
458A GLY* 2.9 58.5 + - - +
476A TYR* 3.5 23.1 + - - -
67B VAL 5.4 0.4 + - - -
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Residues in contact with TYR 430 (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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412A GLY 5.2 0.2 - - - -
413A ASN* 3.1 6.6 - - - +
414A ALA* 2.9 39.2 + - + +
429A ASN* 1.3 75.6 - - - +
431A ARG* 1.3 69.6 + - - +
432A TYR* 3.6 33.1 - - + +
455A SER* 2.7 29.6 + - - -
456A GLN 3.3 17.7 - - - -
457A VAL* 3.6 22.4 - - + -
479A THR* 4.9 1.8 - - + -
480A LYS* 5.7 0.2 - - - -
604A C8E 3.8 38.9 - - - -
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Residues in contact with ARG 431 (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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411A LEU* 5.7 1.0 - - - +
412A GLY 3.8 4.0 - - - -
413A ASN* 3.8 32.7 + - + +
429A ASN* 3.8 18.2 - - + +
430A TYR* 1.3 83.7 - - - +
432A TYR* 1.3 60.1 + - - +
454A ILE* 3.5 9.8 - - + +
455A SER* 3.2 6.2 + - - -
456A GLN* 2.9 37.6 + - + +
67B VAL* 3.7 38.8 - - - +
68B SER* 4.4 1.8 - - - -
77B GLU* 2.4 45.8 + - - +
79B GLN* 5.2 4.9 + - - -
105B THR* 3.3 29.3 + - - +
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Residues in contact with TYR 432 (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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409A LEU* 3.7 36.5 + - + +
410A THR 4.1 6.5 - - - -
411A LEU* 3.5 6.1 - - - +
412A GLY 2.8 40.5 + - - +
430A TYR* 3.6 30.0 - - + +
431A ARG* 1.3 75.3 - - - +
433A ALA* 1.3 67.3 + - - +
434A SER* 3.4 35.8 + - - -
435A PRO* 4.2 5.7 - - + +
453A GLY* 6.1 0.2 - - - -
454A ILE* 3.0 17.3 - - - -
455A SER* 4.4 3.6 - - - -
480A LYS* 5.0 13.5 - - - -
604A C8E 3.8 29.4 + - - -
77B GLU* 4.6 3.0 - - - +
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Residues in contact with ALA 433 (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 3.3 7.4 - - - +
411A LEU* 3.6 8.1 - - + -
432A TYR* 1.3 81.9 - - - +
434A SER* 1.3 65.6 + - - +
437A TYR* 5.0 0.9 - - + -
438A ILE* 4.4 2.2 - - + -
453A GLY* 3.0 9.0 - - - -
454A ILE* 2.9 42.1 + - + +
77B GLU* 4.3 1.3 - - - +
107B PHE* 3.5 32.3 - - + -
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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