Contacts of the strand formed by residues 486 - 494 (chain H) in PDB entry 3SZ9
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 THR 486 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139H TYR* 3.3 20.5 - - + -
156H HIS* 3.6 41.9 - - + +
157H GLU 3.2 8.7 - - - +
159H VAL* 4.4 4.4 - - - +
185H THR* 4.1 7.7 - - - +
482H LEU 3.0 17.1 + - - -
483H GLN* 3.4 13.9 + - - +
484H ALA 3.4 3.0 - - - +
485H TYR* 1.3 79.5 + - - +
487H GLU* 1.3 70.1 + - - +
488H VAL* 4.2 8.1 + - + +
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Residues in contact with GLU 487 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467G GLY 3.2 1.2 - - - +
468G TYR* 3.4 39.6 + - + +
473G SER* 5.3 0.5 - - - -
474G GLY 5.4 0.7 + - - -
475G ARG* 2.8 22.7 + - - +
156H HIS 3.9 0.2 - - - -
157H GLU* 2.7 38.8 + - - +
158H PRO 4.1 12.1 - - - +
159H VAL* 3.5 17.1 - - - +
264H ARG* 2.9 43.4 + - - -
486H THR* 1.3 76.0 - - - +
488H VAL* 1.3 61.2 + - - +
489H LYS 3.6 1.9 + - - -
6801H GAI 4.8 1.6 - - - +
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Residues in contact with VAL 488 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449G GLY 3.8 3.3 - - - +
464G PRO* 4.1 11.4 - - + -
468G TYR* 3.9 1.5 - - - -
475G ARG* 2.8 51.4 + - + +
480G TYR* 3.6 37.0 - - + -
483G GLN* 6.0 0.2 - - - +
154H THR* 3.9 30.1 - - + -
155H ARG 3.7 3.8 - - - +
156H HIS* 4.0 10.5 - - + -
486H THR* 4.4 8.5 - - + +
487H GLU* 1.3 76.2 - - - +
489H LYS* 1.3 61.3 + - - +
490H THR* 5.4 0.2 + - - -
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Residues in contact with LYS 489 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443G SER 2.8 26.5 + - - +
444G GLN* 2.9 9.3 + - - +
446G LEU 2.8 29.1 + - - -
448G ALA 3.4 20.6 - - - +
449G GLY 3.4 3.4 - - - -
451G VAL* 4.0 9.6 - - + -
468G TYR* 3.4 13.7 - - - +
153H TYR 3.8 0.2 - - - +
154H THR* 3.0 5.8 - - - -
155H ARG* 2.9 45.9 + - + +
157H GLU* 2.8 35.5 + - - +
487H GLU 3.6 1.0 + - - -
488H VAL* 1.3 74.1 - - - +
490H THR* 1.3 72.4 + - - +
491H VAL* 3.9 11.7 + - + +
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Residues in contact with THR 490 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449G GLY 2.8 12.0 + - - -
450G THR* 3.2 11.0 - - + -
451G VAL 2.7 32.7 + - - +
463G SER* 4.0 10.8 - - - -
464G PRO* 2.8 48.9 + - + +
475G ARG* 6.0 0.2 - - - -
144H ILE* 5.8 0.2 - - + -
152H SER* 3.7 11.0 - - - +
153H TYR 3.4 7.4 - - - +
154H THR* 3.8 2.0 - - + +
488H VAL* 4.2 0.7 + - - +
489H LYS* 1.3 75.4 - - - +
491H VAL* 1.3 56.4 + - - +
492H THR* 3.5 21.5 - - - +
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Residues in contact with VAL 491 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443G SER* 4.0 20.4 - - - -
451G VAL* 3.3 12.6 - - + +
453G VAL* 4.3 4.7 - - + -
151H PHE 3.7 1.8 - - - +
152H SER* 3.2 2.4 + - - -
153H TYR* 2.7 81.9 + - + +
155H ARG* 4.6 3.1 - - - -
489H LYS* 4.0 23.8 - - + +
490H THR* 1.3 76.0 - - - +
492H THR* 1.3 63.6 + - - +
493H VAL* 3.9 13.2 - - + -
6901H EDO 4.1 7.4 - - - +
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Residues in contact with THR 492 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450G THR* 5.0 0.8 - - - +
451G VAL 3.0 7.0 + - - -
452G TRP* 3.5 20.2 + - + -
453G VAL 3.0 21.5 + - - -
455G CYS* 3.5 7.1 - - - -
458G VAL* 3.9 33.4 + - + +
463G SER* 4.6 1.0 + - - -
146H ILE* 4.6 4.9 - - + +
150H PHE* 4.1 16.6 - - + -
151H PHE 3.5 2.9 - - - -
152H SER* 2.8 23.8 + - - +
490H THR* 3.5 11.9 - - - +
491H VAL* 1.3 72.7 - - - +
493H VAL* 1.3 61.9 + - - +
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Residues in contact with VAL 493 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436F LEU* 4.2 9.4 - - + -
440F ASN* 4.0 18.8 - - - +
453G VAL* 3.8 30.1 - - + -
150H PHE* 3.1 7.6 - - - -
151H PHE* 2.7 56.3 + - + +
153H TYR* 4.4 11.4 - - + +
491H VAL* 3.9 20.9 - - + -
492H THR* 1.3 77.8 - - - +
494H LYS* 1.3 75.5 + - - +
495H VAL* 3.7 0.3 - - - +
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Residues in contact with LYS 494 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436F LEU* 5.1 1.2 - - - +
437F ASP* 4.0 15.9 - - - +
440F ASN* 4.8 1.2 + - - -
285G TRP* 3.7 37.1 - - + +
453G VAL 3.0 12.3 + - - +
454G ASN* 3.4 36.7 + - + +
455G CYS* 4.1 6.7 - - + -
149H ASP* 4.5 4.8 - - - +
150H PHE* 3.8 16.6 - - + -
493H VAL* 1.3 84.1 - - - +
495H VAL* 1.3 71.5 + - - +
496H PRO* 6.4 0.4 - - - -
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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
------------------------------------------------------------
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