Contacts of the strand formed by residues 392 - 399 (chain B) in PDB entry 1XMI
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 VAL 392 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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390B THR* 4.4 2.7 - - + -
391B GLU* 1.3 78.2 - - - +
393B VAL* 1.3 68.7 + - - +
394B MET* 5.2 2.2 - - + -
446B PHE* 3.8 25.8 - - + +
447B LYS* 3.4 3.6 - - - -
448B ILE* 2.9 54.2 + - + +
471B ILE* 4.8 12.1 - - + -
482B ILE* 5.6 0.9 - - + -
483B LYS 3.2 6.5 - - - +
484B HIS* 4.3 9.2 - - + +
568B LEU* 3.6 39.5 - - + -
599B THR* 4.4 1.1 - - + -
601B ILE* 4.7 7.9 - - + -
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Residues in contact with VAL 393 (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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391B GLU* 3.6 23.8 - - + +
392B VAL* 1.3 79.6 - - - +
394B MET* 1.3 66.1 + - - +
395B GLU* 3.9 30.1 - - + +
446B PHE 3.6 7.4 - - - +
447B LYS* 4.3 16.2 - - + +
481B LYS* 3.7 1.2 - - + +
482B ILE* 3.3 5.7 - - - +
483B LYS* 2.7 65.6 + - + +
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Residues in contact with MET 394 (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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392B VAL* 5.2 2.2 - - + -
393B VAL* 1.3 77.6 - - - +
395B GLU* 1.3 65.5 + - - +
397B VAL* 3.9 10.1 - - + -
444B ILE* 3.8 13.0 - - - +
445B ASN* 3.3 6.2 - - - +
446B PHE* 2.9 63.1 + - + +
467B LEU* 3.6 28.0 - - + +
470B MET* 3.7 24.9 - - + -
471B ILE* 3.6 30.1 - - + -
481B LYS 3.4 2.2 - - - -
482B ILE* 3.9 22.7 - - + -
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Residues in contact with GLU 395 (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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393B VAL* 3.9 15.6 - - + +
394B MET* 1.3 77.1 - - - +
396B ASN* 1.3 76.3 + - - +
397B VAL* 3.2 2.5 + - - +
445B ASN* 3.5 4.5 - - - +
480B GLY* 3.2 2.9 - - - -
481B LYS* 2.8 61.6 + - + +
483B LYS* 3.3 25.8 + - - -
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Residues in contact with ASN 396 (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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395B GLU* 1.3 77.4 - - - +
397B VAL* 1.3 61.0 + - - +
398B THR* 3.7 1.2 + - - -
443B ASP* 2.8 34.2 + - - +
444B ILE 3.3 2.7 + - - -
445B ASN* 2.6 29.0 + - - +
479B GLU* 3.3 24.1 - - + +
480B GLY* 3.4 7.1 + - - -
481B LYS* 6.1 0.9 - - - +
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Residues in contact with VAL 397 (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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394B MET* 3.9 6.7 - - + -
395B GLU 3.5 13.2 - - - +
396B ASN* 1.3 72.3 - - - +
398B THR* 1.3 64.0 + - - +
441B LEU* 4.0 1.7 - - - +
442B LYS* 3.5 2.3 - - - -
443B ASP 2.8 21.3 + - - -
444B ILE* 3.0 26.9 + - + +
470B MET* 3.4 38.6 - - + -
477B PRO* 3.7 18.8 - - + -
479B GLU 3.2 2.9 - - - -
481B LYS 3.5 28.3 - - - +
482B ILE* 3.9 12.1 - - + -
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Residues in contact with THR 398 (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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396B ASN 3.7 1.2 + - - -
397B VAL* 1.3 72.0 - - - +
399B ALA* 1.3 63.4 + - - +
400B PHE* 4.3 13.5 - - + -
409B PHE* 4.4 16.4 - - + -
439B PRO* 3.9 17.9 - - + -
441B LEU 3.2 12.1 - - - +
442B LYS* 3.9 9.5 - - + +
443B ASP* 3.3 18.9 + - - +
477B PRO* 3.5 3.6 - - - +
478B SER* 2.8 25.4 + - - -
479B GLU* 3.1 30.8 + - - -
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Residues in contact with ALA 399 (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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398B THR* 1.3 76.7 - - - +
400B PHE* 1.3 65.8 + - - +
439B PRO* 3.3 5.0 - - - +
440B VAL* 2.9 29.0 + - + +
441B LEU* 2.9 12.6 + - + +
470B MET* 3.5 30.5 - - - -
475B LEU* 4.0 14.6 - - + -
476B GLU 3.6 15.5 - - - +
478B SER 4.3 1.6 - - - +
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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