Contacts of the strand formed by residues 486 - 491 (chain D) in PDB entry 5I94
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 GLY 486 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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281D PHE* 4.3 7.5 - - - -
286D CYS* 4.0 10.1 - - - -
481D SER* 3.3 1.6 - - - -
482D GLY 3.1 25.7 + - - +
484D ALA* 3.6 3.8 - - - +
485D GLY* 1.3 78.8 - - - +
487D ILE* 1.3 67.8 + - - +
498D MET* 4.0 9.0 - - - -
499D CYS 3.2 8.5 - - - -
500D TRP* 3.8 8.4 - - - -
510D SER* 5.1 0.5 + - - -
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Residues in contact with ILE 487 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464D MET* 3.8 22.0 - - + -
479D ALA* 4.2 23.8 - - + -
480D LYS 3.6 4.7 - - - +
481D SER* 4.2 8.7 - - - -
486D GLY* 1.3 79.9 - - - +
488D LEU* 1.3 63.9 + - - +
489D LEU* 3.4 7.0 + - + +
497D MET 3.6 1.4 - - - +
498D MET* 3.4 4.8 - - - +
499D CYS* 2.9 38.6 + - + +
510D SER* 4.2 15.9 - - - +
513D GLY* 3.7 33.9 - - - -
514D ILE* 3.7 9.4 - - + +
517D CYS* 4.4 16.2 - - - -
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Residues in contact with LEU 488 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283D LEU* 5.9 1.6 - - + -
286D CYS* 3.9 23.8 - - + +
289D PRO* 4.3 15.9 - - + -
290D LEU* 4.4 18.8 - - + -
426D ALA* 3.7 25.4 - - + +
429D MET* 5.1 3.1 - - + -
430D ALA* 3.7 19.1 - - + +
433D LEU* 4.9 5.8 - - + -
459D MET* 3.8 12.1 - - + +
479D ALA* 3.1 7.4 - - - -
480D LYS 2.9 41.8 + - - +
486D GLY 4.2 0.2 - - - -
487D ILE* 1.3 70.1 - - - +
489D LEU* 1.3 58.1 + - - +
490D VAL* 5.6 0.2 - - + -
497D MET 3.6 4.5 - - - +
498D MET* 3.8 24.0 - - + +
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Residues in contact with LEU 489 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430D ALA* 3.5 1.6 - - - +
471D PHE* 4.3 9.6 - - + -
477D LEU* 3.7 30.5 - - + -
478D PRO 3.6 15.3 - - - +
479D ALA* 4.0 12.1 - - + -
487D ILE* 3.4 8.9 + - + +
488D LEU* 1.3 73.4 - - - +
490D VAL* 1.3 69.6 + - - +
491D VAL* 4.9 3.4 - - + -
496D GLY* 3.4 4.0 - - - -
497D MET* 2.7 75.5 + - + +
499D CYS* 5.5 0.2 - - - -
517D CYS* 4.2 17.3 - - + -
520D LEU* 3.9 20.9 - - + -
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Residues in contact with VAL 490 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430D ALA* 3.5 24.9 - - + +
433D LEU* 4.0 16.6 - - + -
434D ALA* 3.8 24.7 - - + -
456D LEU* 3.8 27.4 - - + -
459D MET* 4.4 8.5 - - + -
477D LEU* 3.4 9.9 - - - +
478D PRO* 3.1 35.2 + - + +
488D LEU* 5.4 0.4 - - + -
489D LEU* 1.3 82.4 - - - +
491D VAL* 1.3 63.7 + - - +
492D PRO* 3.4 13.6 - - + +
495D MET 3.8 2.0 - - - -
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Residues in contact with VAL 491 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434D ALA* 3.7 1.2 - - - +
477D LEU* 3.9 24.9 - - + -
489D LEU* 4.9 7.2 - - + -
490D VAL* 1.3 76.6 - - - +
492D PRO* 1.3 71.1 - - + +
494D VAL* 3.0 24.8 + - + -
495D MET* 2.8 59.7 + - + +
497D MET* 5.9 0.4 - - + -
520D LEU* 4.9 0.7 - - + -
526D PHE* 3.8 35.4 - - + +
542D ARG* 5.6 0.7 - - - +
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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