Contacts of the strand formed by residues 425 - 430 (chain B) in PDB entry 1X11
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 ILE 425 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337B LEU* 4.4 11.7 - - + -
361B VAL* 3.5 43.5 - - + -
365B LYS* 4.7 13.7 - - + +
420B ALA 3.7 0.3 - - - +
421B ASP* 3.3 7.3 - - - +
422B ILE* 3.1 32.1 + - + +
424B ASN* 1.3 102.9 - - - +
426B VAL* 1.3 67.2 + - - +
427B VAL* 3.9 6.1 - - + -
462B VAL* 3.6 17.5 - - + -
463B PHE 3.2 8.3 - - - +
464B GLU* 3.4 28.5 - - + +
468B ALA* 4.5 0.2 - - - -
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Residues in contact with VAL 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390B LEU* 5.6 0.7 - - + -
419B ILE* 3.2 32.3 - - + -
420B ALA 3.4 4.5 - - - +
425B ILE* 1.3 77.1 - - - +
427B VAL* 1.3 62.4 + - - +
428B LEU* 5.9 0.4 - - + -
461B HIS 3.1 4.7 - - - +
462B VAL* 3.4 2.1 - - - -
463B PHE* 2.7 59.4 + - + +
465B SER* 4.7 4.0 - - - -
468B ALA* 3.9 32.5 - - + +
471B ILE* 4.0 30.1 - - + -
472B ALA* 4.6 2.5 - - + -
475B ILE* 5.6 0.2 - - + -
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Residues in contact with VAL 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B ALA* 4.0 24.7 - - + +
360B ALA* 4.0 24.9 - - + -
361B VAL* 3.4 32.3 - - + -
418B TYR* 3.7 2.1 - - - +
419B ILE* 3.3 10.0 - - - +
420B ALA 2.8 37.5 + - - +
422B ILE* 4.3 3.6 - - + -
425B ILE* 3.9 3.8 - - + -
426B VAL* 1.3 75.9 - - - +
428B LEU* 1.3 61.4 + - - +
429B MSE 4.0 12.3 - - + -
460B CYS* 4.4 8.5 - - + -
461B HIS 3.3 7.9 - - - +
462B VAL* 4.5 3.1 - - + -
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Residues in contact with LEU 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390B LEU* 5.9 2.5 - - + -
397B ILE* 4.0 30.5 - - + -
399B VAL* 5.9 1.8 - - + -
411B HIS* 4.3 10.1 - - - +
416B ILE* 4.1 24.0 - - + -
418B TYR 3.7 2.5 - - - -
419B ILE* 4.2 8.3 - - + -
426B VAL* 4.0 1.3 - - + -
427B VAL* 1.3 72.3 - - - +
429B MSE 1.3 63.2 + - - +
430B ALA* 4.0 23.6 - - + -
459B ILE 3.3 3.3 - - - +
460B CYS* 3.4 1.4 - - - -
461B HIS* 2.8 45.6 + - + +
463B PHE* 4.1 27.4 - - + -
475B ILE* 4.4 13.2 - - + -
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Residues in contact with MSE 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342B LEU* 4.0 12.3 - - - -
353B ARG* 3.2 51.6 - - - +
356B GLN* 4.2 4.9 - - - +
357B ALA* 3.6 22.9 - - + +
416B ILE* 3.7 2.6 - - - +
417B SER* 2.9 37.9 + - - +
418B TYR* 2.8 41.7 + - + +
427B VAL* 4.0 8.5 + - + -
428B LEU* 1.3 75.6 - - - +
430B ALA* 1.3 53.2 + - - +
458B MSE 3.4 13.0 - - + -
459B ILE 3.4 2.7 - - - -
460B CYS* 3.6 23.3 - - + -
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Residues in contact with ALA 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411B HIS* 3.5 45.5 - - + +
415B THR 3.3 10.8 - - - +
416B ILE* 4.2 3.1 - - + -
428B LEU* 3.9 10.2 + - + -
429B MSE 1.3 73.7 - - - +
431B ARG* 1.3 57.7 + - - +
458B MSE 3.3 9.1 - - - +
459B ILE* 2.6 41.7 + - + -
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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