Contacts of the strand formed by residues 514 - 518 (chain C) in PDB entry 2UZ1
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 ASP 514 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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512C GLY 4.8 1.9 - - - +
513C ALA* 1.3 71.7 - - - +
515C GLY* 1.3 54.6 + - - +
516C TYR* 4.0 25.1 + - + +
534C HIS* 5.5 1.4 - - - +
536C ARG* 2.7 53.8 + - - +
537C PRO 3.2 16.0 + - - +
538C ALA* 3.2 4.0 - - + +
539C CYS* 2.7 33.7 + - - +
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Residues in contact with GLY 515 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505C HIS* 4.1 27.1 - - - -
508C ALA* 5.0 0.4 - - - -
509C ALA* 5.0 4.8 - - - +
513C ALA 3.3 4.4 + - - -
514C ASP* 1.3 74.3 - - - +
516C TYR* 1.3 67.4 + - - -
539C CYS* 3.4 5.8 - - - -
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Residues in contact with TYR 516 (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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505C HIS* 3.5 6.4 - - - +
514C ASP* 4.0 30.7 + - + +
515C GLY* 1.3 78.2 - - - -
517C HIS* 1.3 57.6 + - - +
518C VAL* 4.3 2.2 - - + -
527C ALA* 3.6 42.8 - - + -
530C GLN* 3.1 40.3 + - - +
531C ALA* 3.9 13.3 + - + -
534C HIS* 5.4 1.6 - - - -
538C ALA* 4.0 12.3 - - + -
539C CYS 2.8 19.7 + - - +
540C ILE* 3.8 16.8 - - + -
541C ASN* 2.8 34.9 + - - +
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Residues in contact with HIS 517 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474C ASN* 5.7 2.2 - - + -
505C HIS* 3.4 35.5 - + + +
516C TYR* 1.3 74.1 - - - +
518C VAL* 1.3 74.9 + - - +
519C ASP* 6.0 1.1 - - + -
523C SER* 5.5 0.3 - - - -
541C ASN* 3.2 34.4 + - - -
543C ALA* 4.7 13.5 - - + -
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Residues in contact with VAL 518 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516C TYR* 4.6 2.2 - - + -
517C HIS* 1.3 88.6 + - - +
519C ASP* 1.3 64.8 + - - +
523C SER* 3.5 35.7 - - - +
524C PHE* 3.8 20.0 - - + +
527C ALA* 3.7 17.3 - - + -
540C ILE* 3.9 7.0 - - + -
541C ASN 2.9 14.6 + - - +
542C VAL* 3.8 23.6 - - + -
543C ALA* 2.9 25.3 + - - +
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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