Contacts of the helix formed by residues 310 - 315 (chain D) in PDB entry 4UI2
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 GLN 310 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188D PRO 3.5 6.3 - - - -
189D LEU 3.5 10.5 - - - +
190D ILE* 3.9 8.8 - - - +
191D ASP* 2.3 60.5 + - + +
192D ASN* 3.1 5.7 - - - +
300D ALA 4.3 3.1 - - - +
303D TYR* 3.8 20.4 - - + +
307D GLN 3.8 11.5 + - - +
308D ASP 2.8 9.3 + - - +
309D LEU* 1.3 80.3 - - - +
311D LEU* 1.3 66.0 + - - +
312D CYS 3.3 0.7 - - - -
313D VAL* 3.2 28.4 + - + +
314D ASN* 3.0 24.3 + - - +
315D GLY 4.8 0.2 - - - -
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Residues in contact with LEU 311 (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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165C LEU* 5.7 4.7 - - + -
171D LEU* 3.6 27.3 - - + +
173D THR* 3.7 2.1 - - - +
183D VAL* 4.1 26.0 - - + -
187D TRP* 4.1 21.3 - - + -
188D PRO 3.0 21.1 + - - +
189D LEU* 3.3 28.4 + - + -
199D VAL* 5.6 0.7 - - + -
309D LEU* 3.7 23.1 - - + -
310D GLN* 1.3 70.3 - - - +
312D CYS* 1.3 59.5 - - - +
315D GLY* 2.9 40.6 + - - +
316D CYS* 4.4 9.6 - - - +
317D PRO* 4.7 0.2 - - + -
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Residues in contact with CYS 312 (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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163C CYS* 2.0 53.2 - - + -
171D LEU* 4.8 0.2 - - - -
173D THR* 3.3 8.0 - - - +
174D PHE* 2.8 46.3 + - + +
189D LEU* 3.0 38.3 + - - +
190D ILE* 3.8 9.0 - - + -
293D ILE* 4.2 4.0 - - - -
311D LEU* 1.3 77.7 - - - +
313D VAL* 1.3 59.4 + - + +
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Residues in contact with VAL 313 (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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173D THR* 4.6 2.3 - - - -
174D PHE* 4.0 21.3 - - + -
175D LYS* 3.4 37.4 - - - +
189D LEU 5.4 0.2 - - - +
300D ALA 4.5 9.4 - - - +
301D MET* 4.4 11.4 - - - -
303D TYR* 3.8 28.7 - - + +
310D GLN* 3.2 34.3 + - + +
312D CYS* 1.3 81.9 - - + +
314D ASN* 1.3 79.2 + - - +
315D GLY 3.5 0.2 - - - -
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Residues in contact with ASN 314 (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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173D THR* 5.0 1.1 - - - -
175D LYS* 5.2 4.3 + - - +
179D GLN* 4.5 2.8 + - - -
303D TYR* 5.7 2.5 - - - -
308D ASP* 2.3 39.7 + - - +
309D LEU* 4.5 1.9 - - + +
310D GLN 3.0 10.4 + - - +
313D VAL* 1.3 92.7 - - - +
315D GLY* 1.3 65.3 - - - +
316D CYS 4.6 2.9 - - - +
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Residues in contact with GLY 315 (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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171D LEU* 4.2 1.3 - - - -
173D THR* 4.0 6.0 - - - +
179D GLN* 3.2 20.2 - - - -
309D LEU* 4.9 3.1 - - - +
310D GLN 4.3 0.5 - - - +
311D LEU* 2.9 37.9 + - - +
313D VAL 3.5 1.4 + - - -
314D ASN* 1.3 86.6 - - - +
316D CYS* 1.3 66.0 + - - -
317D PRO* 3.8 1.7 - - - +
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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