Contacts of the strand formed by residues 400 - 403 (chain Q) in PDB entry 4UJ3
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 TYR 400 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354Q SER* 5.8 0.7 - - - -
356Q GLU* 5.3 18.2 + - + -
373Q CYS* 3.5 19.6 - - - +
391Q ARG* 4.0 53.2 - - + +
392Q ILE 3.5 6.1 - - - +
393Q LYS* 3.2 50.4 + - + +
397Q SER 4.6 1.6 - - - -
398Q SER* 3.6 14.2 + - - -
399Q ASN* 1.3 74.8 - - - +
401Q TYR* 1.3 60.2 + - - +
402Q TYR* 4.0 7.2 + - + -
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Residues in contact with TYR 401 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140M ARG* 5.2 3.6 + - - -
1182M SO4 3.4 22.4 + - - -
340Q LEU* 3.9 31.2 - - + -
372Q GLU* 3.3 36.1 - - + -
373Q CYS* 3.4 21.8 - - - -
380Q ALA* 3.9 11.4 - - + -
391Q ARG* 3.4 2.0 - - - -
392Q ILE* 2.8 59.3 + - + +
394Q LEU* 4.3 21.6 - - + +
397Q SER* 4.8 3.2 + - - -
399Q ASN* 3.3 30.4 + - + +
400Q TYR* 1.3 72.8 - - - +
402Q TYR* 1.3 63.7 + - - +
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Residues in contact with TYR 402 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358Q VAL* 4.9 15.5 - - + +
369Q SER* 6.1 0.9 - - - -
373Q CYS* 2.8 14.0 + - + +
374Q GLY 3.7 16.6 - - - -
375Q GLY* 3.3 18.6 - - - +
376Q PRO* 3.3 46.9 - - + +
378Q LYS 4.1 1.3 - - - +
380Q ALA* 2.8 32.1 + - - +
388Q CYS* 4.0 17.9 - - + -
390Q HIS 3.7 4.5 - - - -
391Q ARG* 3.3 43.8 + - + -
400Q TYR* 4.4 5.8 - - + -
401Q TYR* 1.3 72.3 - - - +
403Q ILE* 1.3 59.2 + - - +
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Residues in contact with ILE 403 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379Q CYS* 4.2 1.8 - - - -
380Q ALA* 4.3 4.3 - - + -
381Q LEU* 3.2 42.4 - - + +
388Q CYS* 3.3 19.3 - - - +
389Q LYS 4.1 2.6 + - - -
390Q HIS* 3.2 22.6 + - + +
392Q ILE* 3.5 39.5 - - + -
401Q TYR* 3.7 4.7 - - + +
402Q TYR* 1.3 85.2 - - - +
404Q SER* 1.3 71.4 + - - +
407Q CYS* 3.2 25.4 - - + -
408Q ARG* 3.5 15.3 - - + +
411Q ILE* 5.0 1.1 - - + -
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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