Contacts of the helix formed by residues 310 - 319 (chain A) in PDB entry 4UAL
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 SER 310 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174A GLU* 2.6 37.1 + - - -
308A ASP 4.2 0.2 - - - -
309A VAL* 1.3 72.7 - - - +
311A GLU* 1.3 64.5 + - - +
312A GLU* 3.4 17.9 + - - +
313A ALA 3.0 15.9 + - - -
314A LYS* 3.0 25.1 + - - +
341A PHE* 4.7 0.3 - - - -
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Residues in contact with GLU 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309A VAL 3.9 2.3 + - - +
310A SER* 1.3 74.2 - - - +
312A GLU* 1.3 66.7 + - - +
314A LYS* 3.5 29.7 + - - +
315A ASP* 2.9 28.9 + - - +
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Residues in contact with GLU 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A SER* 3.4 19.3 + - - +
311A GLU* 1.3 81.7 + - - +
313A ALA* 1.3 64.9 + - - +
315A ASP* 3.3 4.6 + - - -
316A LEU* 3.1 18.9 + - - +
339A HIS* 3.2 13.9 - - - -
340A ALA* 3.7 26.5 - - + +
341A PHE* 3.8 23.4 - - + +
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Residues in contact with ALA 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A GLU* 3.6 13.5 - - - +
271A MET* 3.4 17.0 - - + +
275A LEU* 3.8 14.4 - - + -
309A VAL* 4.0 4.0 - - + -
310A SER* 3.0 22.1 + - - +
312A GLU* 1.3 74.8 - - - +
314A LYS* 1.3 65.8 + - - +
316A LEU 3.3 1.2 + - - -
317A ILE* 3.0 24.2 + - - +
341A PHE* 3.6 21.5 - - + -
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Residues in contact with LYS 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276A TYR* 3.6 19.9 + - - +
302A PHE* 3.4 54.4 - - + +
306A VAL 5.3 6.1 + - - -
309A VAL* 3.7 24.2 - - + +
310A SER 3.0 12.5 + - - +
311A GLU* 3.9 27.8 + - - +
313A ALA* 1.3 75.9 - - - +
315A ASP* 1.3 61.6 + - - +
317A ILE* 3.4 1.2 + - - -
318A GLN* 3.0 24.1 + - - +
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Residues in contact with ASP 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311A GLU 2.9 17.9 + - - +
312A GLU* 3.6 7.9 - - - +
313A ALA 3.2 0.4 - - - -
314A LYS* 1.3 77.3 - - - +
316A LEU* 1.3 62.5 + - - +
318A GLN* 3.3 16.0 + - - +
319A ARG* 3.0 60.4 + - - +
339A HIS* 2.8 25.2 + - + +
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Residues in contact with LEU 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A ILE* 4.8 3.1 - - + -
271A MET* 3.7 19.7 - - + -
312A GLU 3.1 11.1 + - - +
313A ALA 3.3 3.6 + - - +
315A ASP* 1.3 74.0 - - - +
317A ILE* 1.3 66.5 + - - +
319A ARG* 3.0 11.1 + - - +
320A LEU* 3.2 23.3 + - + +
328A LEU* 3.5 30.1 - - + -
336A PHE* 4.3 7.9 - - + -
339A HIS* 3.5 24.4 + - + +
341A PHE* 3.5 31.2 - - + -
342A PHE* 3.7 19.7 - - + -
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Residues in contact with ILE 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268A GLY 4.5 1.8 - - - +
271A MET* 4.0 26.9 - - + -
272A TYR* 3.9 26.7 - - + +
275A LEU* 4.4 9.2 - - + -
276A TYR* 4.2 11.2 - - + -
300A PHE* 3.9 16.8 - - + -
302A PHE* 3.8 28.5 - - + -
309A VAL* 5.4 0.4 - - + -
313A ALA 3.0 22.5 + - - +
314A LYS* 3.7 4.7 - - - +
315A ASP 3.3 0.2 - - - -
316A LEU* 1.3 76.2 - - - +
318A GLN* 1.3 55.6 + - - +
319A ARG 3.1 0.2 - - - -
320A LEU* 3.0 8.7 + - - +
321A ILE* 2.7 48.8 + - + -
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Residues in contact with GLN 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300A PHE* 4.4 10.9 - - + -
302A PHE* 3.5 31.6 - - + -
314A LYS* 3.0 19.1 + - - +
315A ASP* 3.6 17.5 - - - +
316A LEU 3.2 0.4 - - - -
317A ILE* 1.3 75.8 - - - +
319A ARG* 1.3 62.2 + - + +
320A LEU 3.3 1.8 - - - -
321A ILE 3.9 5.6 - - - +
322A CYS* 3.2 23.7 - - - +
326A ARG* 5.7 1.0 - - - +
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Residues in contact with ARG 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315A ASP* 3.0 42.2 + - - +
316A LEU* 3.0 10.3 + - - +
318A GLN* 1.3 80.2 - - + +
320A LEU* 1.3 60.8 + - - +
322A CYS* 3.5 8.5 - - - -
326A ARG* 4.1 19.4 - - - +
327A ARG* 3.5 2.9 - - - -
328A LEU* 2.9 54.5 + - + +
339A HIS* 4.3 10.7 - - - +
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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