Contacts of the strand formed by residues 486 - 494 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139K TYR* 3.5 29.4 + - + -
156K HIS* 4.2 17.1 - - + +
157K GLU 3.2 12.3 - - - +
159K VAL* 3.7 9.3 - - - +
185K THR* 3.9 20.2 - - + +
482K LEU 3.3 16.5 + - - +
483K GLN* 3.4 15.8 + - - +
484K ALA 3.4 1.9 - - - -
485K TYR* 1.3 85.5 - - - +
487K LYS* 1.3 61.5 + - - +
488K VAL* 4.4 6.2 + - - +
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Residues in contact with LYS 487 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155K ARG 3.5 0.9 - - - +
156K HIS* 3.4 5.4 - - - -
157K GLU* 2.7 48.9 + - + +
158K PRO 4.0 10.5 - - - +
159K VAL* 2.7 48.7 + - + +
239K ASP* 4.6 7.9 + - - +
486K THR* 1.3 73.9 - - - +
488K VAL* 1.3 64.4 + - - +
489K LYS* 3.9 0.4 + - + -
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Residues in contact with VAL 488 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154K THR* 4.0 18.8 - - + -
155K ARG 3.7 2.5 - - - -
156K HIS* 4.0 10.5 - - + -
486K THR* 5.2 6.1 - - - +
487K LYS* 1.3 78.3 - - - +
489K LYS* 1.3 62.4 + - - +
490K THR* 4.2 1.0 + - - +
449L GLY* 3.9 13.0 - - - +
464L PRO* 4.5 11.9 - - + -
480L TYR* 3.5 48.9 - - + +
483L GLN* 6.1 0.2 - - - +
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Residues in contact with LYS 489 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153K TYR 3.8 0.2 - - - +
154K THR* 3.0 6.2 - - - -
155K ARG* 2.9 49.3 + - + +
157K GLU* 3.0 36.0 + - + +
487K LYS* 3.9 0.4 + - + -
488K VAL* 1.3 74.3 - - - +
490K THR* 1.3 69.8 + - - +
491K VAL* 4.1 12.1 + - + +
443L SER 3.2 16.3 + - - +
444L GLN* 2.9 24.5 + - - +
446L LEU 2.8 29.4 + - - -
447L GLN* 4.8 2.7 - - - +
448L ALA 3.5 22.4 - - - +
449L GLY 3.4 3.6 - - - -
451L VAL* 4.6 2.7 - - + -
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Residues in contact with THR 490 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144K ILE* 5.3 0.2 - - + -
152K SER* 3.6 22.4 - - - +
153K TYR 3.4 6.3 - - - +
154K THR* 3.8 5.8 - - + +
488K VAL* 4.7 1.9 + - - +
489K LYS* 1.3 76.6 - - - +
491K VAL* 1.3 66.2 + - - +
492K THR* 3.7 9.9 - - - +
449L GLY 2.7 15.4 + - - -
450L THR* 3.1 9.9 - - + +
451L VAL 2.8 24.9 + - - -
463L SER* 4.5 4.5 - - - -
464L PRO* 3.2 50.5 + - + +
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Residues in contact with VAL 491 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151K PHE 3.7 1.7 - - - +
152K SER* 3.3 2.1 - - - -
153K TYR* 2.8 76.3 + - + +
155K ARG* 5.3 2.9 - - - +
489K LYS* 4.1 23.3 - - + +
490K THR* 1.3 76.6 - - - +
492K THR* 1.3 64.6 + - - +
493K VAL* 3.9 14.8 - - + -
443L SER* 3.9 23.8 - - - +
451L VAL* 3.3 17.5 - - + +
453L VAL* 4.6 2.2 - - + -
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Residues in contact with THR 492 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146K ILE* 4.6 3.8 - - + -
150K PHE* 4.0 17.5 - - + -
151K PHE 3.5 1.6 - - - -
152K SER* 3.1 28.4 + - - -
490K THR* 3.7 9.9 - - - +
491K VAL* 1.3 73.4 - - - +
493K VAL* 1.3 58.2 + - - +
450L THR* 4.8 2.6 - - - +
451L VAL 2.8 9.9 + - - +
452L TRP* 3.2 23.1 + - + -
453L VAL 2.8 28.8 + - - -
455L CYS* 3.6 4.3 - - - -
458L VAL* 4.0 29.6 + - + +
463L SER* 4.7 2.6 + - - -
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Residues in contact with VAL 493 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436I LEU* 4.4 8.3 - - + -
440I ASN* 3.9 21.5 - - - +
150K PHE* 3.2 6.5 - - - -
151K PHE* 2.7 51.4 + - + +
153K TYR* 4.7 8.5 - - + -
491K VAL* 3.9 15.0 - - + -
492K THR* 1.3 77.0 - - - +
494K LYS* 1.3 76.6 - - - +
495K VAL* 3.4 2.4 + - + +
453L VAL* 3.7 35.4 - - + -
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Residues in contact with LYS 494 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437I ASP* 4.1 14.4 - - - +
440I ASN* 4.8 0.9 + - - -
149K ASP* 4.3 8.6 + - - +
150K PHE* 3.8 15.9 - - + -
493K VAL* 1.3 83.2 - - - +
495K VAL* 1.3 69.0 + - - +
496K PRO 5.9 0.2 + - - -
285L TRP* 3.5 36.5 - - + +
453L VAL 2.9 13.1 + - - +
454L ASN* 3.1 41.9 + - + +
455L CYS* 4.1 7.9 - - + -
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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