Contacts of the strand formed by residues 316 - 319 (chain D) 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 LEU 316 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181A VAL* 4.0 2.0 - - - +
183A SER* 5.4 2.5 - - - -
193D ASP* 3.6 39.9 - - - +
196D GLN* 3.7 31.6 - - + +
197D ALA* 3.6 27.4 - - + +
200D LEU* 4.7 3.4 - - + -
298D VAL 3.3 1.8 + - - -
299D ILE* 3.5 18.2 - - + -
300D GLN 3.0 27.9 + - - +
314D ILE* 3.6 5.5 - - - +
315D ALA* 1.3 82.0 - - + +
317D GLY* 1.3 61.4 + - - +
318D ILE* 3.9 16.6 - - + -
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Residues in contact with GLY 317 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A VAL* 3.8 15.2 - - - +
182A LEU* 3.8 0.7 - - - +
183A SER* 2.9 34.3 + - - +
300D GLN 3.7 2.5 - - - -
308D LEU* 3.7 13.9 - - - +
314D ILE* 3.5 18.8 - - - -
316D LEU* 1.3 73.8 - - - +
318D ILE* 1.3 62.1 + - - -
319D VAL 4.1 0.2 + - - -
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Residues in contact with ILE 318 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A SER* 4.6 3.1 - - - -
189D PRO* 3.8 34.5 - - + -
193D ASP* 3.9 36.6 - - + +
194D LEU* 5.4 1.6 - - + -
197D ALA* 4.7 4.3 - - + -
299D ILE* 4.3 6.7 - - + -
300D GLN 2.9 12.1 + - - +
301D VAL* 3.3 21.7 - - + -
302D ASP 3.1 24.9 + - - +
308D LEU* 3.8 3.6 - - - +
316D LEU* 3.9 28.0 - - + -
317D GLY* 1.3 75.7 - - - +
319D VAL* 1.3 64.1 + - - +
320D ALA* 3.6 11.6 + - + -
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Residues in contact with VAL 319 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A SER* 5.1 7.9 - - - -
152A ALA 6.1 1.3 - - - +
182A LEU* 3.7 18.2 - - + -
183A SER* 5.2 3.8 - - - +
185A HIS 5.3 3.3 + - - +
187A ALA* 3.3 22.9 + - + +
189D PRO* 5.4 0.3 - - - +
302D ASP 3.3 4.9 - - - +
303D PRO* 3.7 24.0 - - + +
305D ALA* 3.7 17.7 - - + +
308D LEU* 3.6 22.4 - - + -
317D GLY 4.1 0.8 + - - -
318D ILE* 1.3 72.1 - - - +
320D ALA* 1.3 68.1 + - - +
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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