Contacts of the strand formed by residues 392 - 399 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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390A THR* 4.5 1.3 - - + -
391A GLU* 1.3 78.2 - - - +
393A VAL* 1.3 68.0 + - - +
394A MET* 5.2 2.7 - - + -
446A PHE* 3.8 22.6 - - + +
447A LYS* 3.4 2.3 - - - -
448A ILE* 2.8 53.5 + - + +
471A ILE* 4.8 12.8 - - + -
482A ILE* 5.4 0.7 - - + -
483A LYS 3.3 7.6 - - - +
484A HIS* 4.2 10.3 - - + +
568A LEU* 3.7 38.1 - - + -
599A THR* 4.2 2.7 - - + -
601A ILE* 4.6 9.2 - - + -
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Residues in contact with VAL 393 (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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391A GLU* 4.3 17.5 - - + +
392A VAL* 1.3 82.2 - - - +
394A MET* 1.3 66.9 + - - +
395A GLU* 4.0 26.2 - - + +
446A PHE 3.4 9.0 - - - +
447A LYS* 3.8 28.5 - - + +
481A LYS 3.6 1.1 - - - +
482A ILE* 3.3 5.7 - - - +
483A LYS* 2.8 58.5 + - + +
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Residues in contact with MET 394 (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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392A VAL* 5.2 1.1 - - + -
393A VAL* 1.3 78.1 - - - +
395A GLU* 1.3 65.3 + - - +
397A VAL* 3.8 14.6 - - + -
444A ILE* 3.8 13.7 - - - +
445A ASN* 3.3 4.5 - - - +
446A PHE* 2.8 67.5 + - + +
467A LEU* 3.7 15.3 - - + +
470A MET* 3.7 34.3 - - + -
471A ILE* 3.7 30.7 - - + -
481A LYS 3.3 3.4 - - - -
482A ILE* 4.2 20.2 - - + -
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Residues in contact with GLU 395 (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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393A VAL* 4.0 18.7 - - + +
394A MET* 1.3 76.8 - - - +
396A ASN* 1.3 74.2 + - - +
397A VAL* 3.2 2.1 + - - +
445A ASN* 3.5 5.2 - - - +
480A GLY* 3.1 3.1 - - - -
481A LYS* 2.8 70.9 + - + +
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Residues in contact with ASN 396 (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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395A GLU* 1.3 79.0 - - - +
397A VAL* 1.3 61.6 + - - +
398A THR* 3.7 2.3 + - - -
443A ASP* 3.2 29.3 + - - +
444A ILE 3.3 3.1 + - - -
445A ASN* 2.8 26.1 + - - +
479A GLU* 3.4 14.2 - - + +
480A GLY* 3.2 16.0 + - - -
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Residues in contact with VAL 397 (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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394A MET* 3.8 13.2 - - + -
395A GLU 3.6 12.1 - - - +
396A ASN* 1.3 75.7 - - - +
398A THR* 1.3 60.7 + - - +
441A LEU* 4.3 0.6 - - + -
442A LYS* 3.5 2.1 + - - -
443A ASP 2.8 24.6 + - - -
444A ILE* 2.9 28.0 + - + +
470A MET* 3.4 38.1 - - + -
477A PRO* 4.0 9.9 - - + -
479A GLU 3.2 8.3 - - - +
480A GLY 4.4 0.9 - - - -
481A LYS 3.5 30.1 - - - +
482A ILE* 3.9 9.0 - - + -
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Residues in contact with THR 398 (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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396A ASN 3.7 1.4 + - - -
397A VAL* 1.3 71.4 - - - +
399A ALA* 1.3 65.1 + - - +
400A PHE* 4.5 6.1 - - + -
409A PHE* 4.2 23.2 - - + -
439A PRO* 4.1 16.4 - - + -
441A LEU 3.3 13.0 - - - +
442A LYS* 3.9 10.0 - - + +
443A ASP* 3.2 18.9 + - - +
477A PRO* 3.5 2.1 - - - +
478A SER* 2.8 26.6 + - - -
479A GLU* 3.0 33.9 + - - -
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Residues in contact with ALA 399 (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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398A THR* 1.3 76.9 - - - +
400A PHE* 1.3 66.3 + - - +
439A PRO* 3.4 4.9 - - - +
440A VAL* 2.9 26.8 + - + +
441A LEU* 2.9 15.0 + - + +
470A MET* 3.6 27.4 - - - -
475A LEU* 4.0 13.7 - - + -
476A GLU 3.6 18.8 - - - +
477A PRO* 4.1 0.2 - - + -
478A SER 4.3 1.8 - - - +
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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