Contacts of the strand formed by residues 486 - 494 (chain C) in PDB entry 1ZUM
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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139C TYR* 3.8 15.6 - - + +
156C HIS* 3.4 32.9 + - + +
157C GLU 3.3 11.7 + - - +
159C VAL* 3.5 6.4 - - - +
185C THR* 3.9 14.2 - - - +
264C ARG* 3.6 13.0 + - - -
482C LEU 3.8 12.0 + - - -
483C GLN* 3.4 14.1 + - - +
484C ALA 3.3 1.8 - - - -
485C TYR* 1.3 80.6 + - - +
487C LYS* 1.3 76.4 + - - +
488C VAL* 4.3 5.1 + - + +
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Residues in contact with LYS 487 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155C ARG 3.5 1.9 - - - +
157C GLU* 2.8 36.6 + - + +
158C PRO 3.9 11.2 - - - +
159C VAL* 2.8 48.6 + - + +
239C ASP* 4.7 7.1 + - - +
264C ARG* 4.6 7.9 - - - +
486C THR* 1.3 79.2 - - - +
488C VAL* 1.3 59.4 + - - +
489C LYS 3.8 0.5 + - - -
467D GLY 5.3 0.2 - - - -
468D TYR* 3.9 64.5 - - + +
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Residues in contact with VAL 488 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154C THR* 3.9 28.9 - - + -
155C ARG 3.6 4.7 - - - +
156C HIS* 4.0 8.7 - - + +
486C THR* 5.0 5.4 - - + +
487C LYS* 1.3 74.1 - - - +
489C LYS* 1.3 63.3 + - - +
490C THR* 4.6 0.7 + - - +
449D GLY* 3.9 8.5 - - - +
464D PRO* 4.5 12.1 - - + -
466D GLY* 5.9 2.1 + - - -
468D TYR* 3.9 11.1 - - - -
480D TYR* 3.6 43.1 - - + +
483D GLN* 5.9 0.2 - - - +
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Residues in contact with LYS 489 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153C TYR 3.8 0.2 - - - +
154C THR* 3.0 6.1 - - - -
155C ARG* 2.8 45.7 + - + +
157C GLU* 3.2 24.9 + - - +
487C LYS 3.8 0.8 + - - -
488C VAL* 1.3 73.4 - - - +
490C THR* 1.3 70.6 + - - +
491C VAL* 3.9 13.4 + - + +
443D SER 2.9 25.4 + - - +
444D GLN* 3.2 15.2 + - - +
446D LEU 2.7 29.4 + - - -
447D GLN* 4.9 0.6 - - - +
448D ALA 3.4 19.5 - - - +
449D GLY 3.5 3.6 - - - -
451D VAL* 4.2 5.6 - - + -
468D TYR* 3.0 22.4 - - - +
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Residues in contact with THR 490 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152C SER* 3.9 11.0 - - - +
153C TYR 3.4 6.3 - - - +
154C THR* 3.7 5.6 - - + +
488C VAL* 4.1 1.8 + - - +
489C LYS* 1.3 76.7 - - - +
491C VAL* 1.3 58.3 + - - +
492C THR* 3.7 19.3 - - - +
449D GLY 2.8 14.0 + - - -
450D THR* 3.1 12.5 - - + +
451D VAL 2.8 30.8 + - - -
463D SER* 4.4 10.5 - - - -
464D PRO* 3.1 46.4 + - + +
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Residues in contact with VAL 491 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151C PHE 3.7 1.9 - - - +
152C SER* 3.4 1.7 - - - -
153C TYR* 2.9 76.4 + - + +
155C ARG* 4.7 2.5 - - - -
489C LYS* 3.9 24.0 - - + +
490C THR* 1.3 75.3 - - - +
492C THR* 1.3 64.1 + - - +
493C VAL* 4.1 13.9 - - + -
3113C EDO 4.2 6.5 - - - +
443D SER* 3.9 21.3 - - - -
451D VAL* 3.2 14.1 - - + +
453D VAL* 4.3 3.8 - - + -
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Residues in contact with THR 492 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146C ILE* 4.4 7.1 - - + +
150C PHE* 4.1 17.9 - - + -
151C PHE 3.5 4.3 - - - +
152C SER* 2.9 20.6 + - - -
490C THR* 3.7 11.3 + - - +
491C VAL* 1.3 70.8 - - - +
493C VAL* 1.3 62.7 + - - +
450D THR* 5.0 1.8 - - - +
451D VAL 2.9 9.1 + - - -
452D TRP* 3.3 27.5 + - + -
453D VAL 3.0 21.8 + - - -
455D CYS* 3.4 4.9 - - - -
458D VAL* 4.1 27.8 + - + +
463D SER* 4.6 2.4 + - - -
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Residues in contact with VAL 493 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436A LEU* 4.3 9.2 - - + -
440A ASN* 4.1 19.1 - - - +
150C PHE* 3.2 6.0 - - - -
151C PHE* 2.8 53.2 + - + +
153C TYR* 4.6 10.8 - - + +
491C VAL* 4.1 12.8 - - + -
492C THR* 1.3 76.1 - - - +
494C LYS* 1.3 78.2 + - - +
495C VAL* 3.4 1.3 + - + +
453D VAL* 3.7 37.2 - - + +
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Residues in contact with LYS 494 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436A LEU* 4.9 2.6 - - - +
437A ASP* 4.2 15.2 - - - +
440A ASN* 4.7 0.7 + - - -
149C ASP* 4.3 5.1 - - + +
150C PHE* 3.8 16.8 - - + -
493C VAL* 1.3 83.8 - - - +
495C VAL* 1.3 69.3 + - - +
285D TRP* 3.5 36.9 - - + +
453D VAL 3.0 11.7 + - - +
454D ASN* 3.4 36.2 - - + +
455D CYS* 4.1 9.3 - - + -
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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