Contacts of the strand formed by residues 507 - 515 (chain C) in PDB entry 5ZHU
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 ASN 507 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421C TYR* 3.5 31.1 - - - -
500C GLN* 3.6 33.5 + - + +
501C ALA 3.6 2.5 - - - -
502C HIS* 4.1 6.6 - - - +
506C GLN* 1.3 90.2 + - - +
508C TYR* 1.3 70.4 + - - +
509C THR* 4.3 0.5 + - - -
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Residues in contact with TYR 508 (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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353C ALA* 4.1 13.5 - - + -
408C VAL* 4.0 27.4 - - + -
410C THR* 2.9 29.8 + - - +
411C PRO* 4.6 8.3 - - + -
412C GLU* 4.1 8.7 + - - -
415C LYS* 5.4 3.6 - - + +
500C GLN* 3.4 2.6 - - - -
501C ALA* 2.6 52.8 + - + +
503C ALA* 3.1 31.8 + - + -
504C GLN* 4.5 5.2 + - - +
506C GLN* 2.2 46.4 + - + +
507C ASN* 1.3 78.5 - - - +
509C THR* 1.3 63.4 + - - +
510C LEU* 3.6 1.0 + - + +
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Residues in contact with THR 509 (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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351C LYS 4.9 6.8 + - - -
352C TRP* 3.5 18.5 - - + -
353C ALA* 2.9 29.2 + - - +
498C ALA* 4.2 8.7 - - + +
499C LEU 3.5 10.8 - - - +
500C GLN* 4.5 8.5 + - - +
507C ASN 4.3 0.9 + - - -
508C TYR* 1.3 71.9 - - - +
510C LEU* 1.3 61.3 + - - +
511C ALA 4.0 5.6 - - - +
512C ALA* 3.8 28.5 - - + -
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Residues in contact with LEU 510 (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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352C TRP* 3.5 21.9 - - - +
353C ALA* 3.1 27.2 - - + +
354C THR 4.4 1.6 - - - +
355C LEU* 3.8 36.8 - - + -
365C MET* 3.6 11.5 - - - +
366C LEU* 4.3 8.3 - - + -
408C VAL* 5.0 1.6 - - + -
420C PHE* 3.9 12.8 - - + -
499C LEU* 2.8 38.4 + - + +
501C ALA* 3.5 34.8 - - + -
508C TYR 3.9 2.2 - - - +
509C THR* 1.3 78.3 - - - +
511C ALA* 1.3 60.6 + - - +
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Residues in contact with ALA 511 (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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352C TRP* 4.2 11.2 - - + -
365C MET* 4.4 5.2 - - + -
366C LEU* 4.0 12.8 - - + -
368C TYR* 3.4 42.7 - - + -
498C ALA* 3.3 1.4 - - - +
499C LEU* 2.5 36.7 + - + +
509C THR* 3.8 1.3 - - - +
510C LEU* 1.3 80.9 - - - +
512C ALA* 1.3 59.6 + - - +
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Residues in contact with ALA 512 (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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346C PRO* 3.6 1.9 - - - +
347C HIS* 2.7 54.1 + - + +
348C GLN* 6.1 0.2 - - - +
352C TRP* 3.5 13.3 - - - +
368C TYR* 3.8 1.6 - - - -
496C VAL* 5.1 2.0 - - + -
497C VAL 3.4 7.0 - - - +
498C ALA* 3.6 19.7 - - + -
509C THR* 3.8 13.2 - - + -
511C ALA* 1.3 77.8 - - - +
513C GLN* 1.3 57.4 + - - +
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Residues in contact with GLN 513 (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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344C TRP* 3.2 29.6 - - + +
345C GLN* 3.5 10.3 + - - -
346C PRO* 3.5 33.4 - - - +
347C HIS* 4.3 1.8 - - - -
352C TRP* 5.3 3.6 - - - -
368C TYR* 3.8 28.9 + - + +
369C ARG* 6.0 0.4 - - - -
370C VAL* 3.5 30.3 - - + +
496C VAL* 3.5 1.2 - - - +
497C VAL 3.0 33.5 + - - +
512C ALA* 1.3 74.1 + - - +
514C ILE* 1.3 60.1 + - - +
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Residues in contact with ILE 514 (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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344C TRP* 3.4 4.3 - - - -
345C GLN* 2.9 53.4 + - + +
346C PRO 4.0 1.8 - - - +
347C HIS* 3.7 39.0 - - + +
427C VAL* 4.3 8.7 - - + -
432C LEU* 5.9 1.3 - - + -
494C MET* 3.5 32.1 - - + -
495C LEU 3.4 4.0 - - - +
496C VAL* 3.7 24.2 - - + +
513C GLN* 1.3 72.4 - - - +
515C SER* 1.3 72.1 + - - +
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Residues in contact with SER 515 (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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342C ILE* 3.6 19.5 - - - -
343C LYS 3.7 4.9 - - - -
344C TRP* 3.3 21.2 - - - -
494C MET* 3.7 18.9 - - - +
495C LEU* 2.7 38.4 + - - -
514C ILE* 1.3 82.9 - - - +
516C GLU* 1.3 70.9 + - - +
518C ILE* 3.5 7.6 - - - +
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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