Contacts of the helix formed by residues 304 - 314 (chain A) in PDB entry 5L0P
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 ALA 304 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303A SER* 1.3 72.9 - - - +
305A GLU* 1.3 58.0 + - - +
307A LEU 3.1 1.9 + - - -
308A TYR* 2.8 25.9 + - - +
320A LEU* 4.7 1.3 - - - -
323A VAL* 3.3 13.6 - - + +
324A TYR* 3.5 47.8 - - + +
327A LEU* 3.8 23.6 - - + -
344A GLY 5.0 2.3 + - - +
346A SER 4.1 4.6 + - - -
348A PHE* 4.2 6.8 - - + -
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Residues in contact with GLU 305 (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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303A SER* 3.4 5.0 + - - +
304A ALA* 1.3 75.8 - - - +
306A ASP* 1.3 63.0 + - - +
308A TYR* 3.2 5.0 + - + +
309A LYS* 2.8 30.2 + - - +
320A LEU* 4.1 27.2 - - + +
324A TYR* 3.7 12.8 - - - +
343A GLY 5.3 0.2 - - - +
344A GLY 2.9 23.6 - - - +
345A LYS* 4.1 18.9 + - - +
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Residues in contact with ASP 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A ASN* 5.3 2.5 - - - +
302A VAL* 3.8 17.4 - - + +
303A SER* 3.5 19.6 + - - +
304A ALA 3.4 0.2 - - - -
305A GLU* 1.3 76.0 - - - +
307A LEU* 1.3 61.1 + - - +
309A LYS* 3.8 6.4 - - - +
310A ARG* 2.8 32.9 + - - +
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Residues in contact with LEU 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A ILE* 3.4 35.4 - - + +
293A VAL* 3.5 27.8 - - + -
294A LEU* 4.2 8.1 - - + -
302A VAL* 3.9 21.0 - - + +
303A SER 3.0 14.4 + - - +
304A ALA 3.4 8.3 - - - +
306A ASP* 1.3 77.2 - - - +
308A TYR* 1.3 59.0 + - - +
310A ARG* 3.3 4.7 + - - +
311A LEU* 2.8 50.7 + - + +
323A VAL* 4.0 6.3 - - + -
327A LEU* 3.7 22.2 - - + -
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Residues in contact with TYR 308 (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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304A ALA 2.8 9.6 + - - +
305A GLU 3.3 9.9 - - - +
307A LEU* 1.3 75.9 - - - +
309A LYS* 1.3 60.1 + - + +
311A LEU* 2.8 27.5 + - + +
312A ILE* 2.8 48.2 + - + +
318A ILE 3.0 28.5 - - - -
319A GLY* 4.2 1.8 - - - -
320A LEU* 3.4 47.3 - - + -
323A VAL* 4.2 14.1 - - + +
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Residues in contact with LYS 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A GLU 2.8 18.4 + - - +
306A ASP* 3.8 7.6 - - - +
308A TYR* 1.3 75.1 - - + +
310A ARG* 1.3 61.2 + - - +
312A ILE* 3.5 17.1 - - + +
313A ASP* 3.2 23.6 + - - +
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Residues in contact with ARG 310 (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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293A VAL* 3.9 23.6 - - + -
296A GLU* 3.0 36.5 + - - +
299A ASN* 3.9 13.2 - - - +
306A ASP 2.8 21.6 + - - +
307A LEU* 3.4 7.0 - - - +
309A LYS* 1.3 70.8 - - - +
311A LEU* 1.3 65.3 + - - +
313A ASP* 3.7 16.3 + - - +
314A MET* 3.3 62.3 + - - +
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Residues in contact with LEU 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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289A LYS* 3.8 31.0 - - + +
290A ILE* 3.8 15.3 - - + -
293A VAL* 3.7 20.9 - - + -
307A LEU* 2.8 33.3 + - + +
308A TYR* 2.8 15.7 + - + +
310A ARG* 1.3 70.3 - - - +
312A ILE* 1.3 61.2 + - + +
314A MET* 3.0 18.9 + - - +
316A GLU* 3.2 35.4 + - + +
318A ILE* 4.4 17.9 - - + +
323A VAL* 4.0 18.4 - - + -
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Residues in contact with ILE 312 (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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308A TYR* 2.8 58.9 + - + +
309A LYS* 3.5 15.5 - - + +
311A LEU* 1.3 70.5 - - - +
313A ASP* 1.3 59.6 + - - +
315A GLY* 2.5 27.7 + - - -
316A GLU 3.9 14.2 + - - +
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Residues in contact with ASP 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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309A LYS 3.2 13.5 + - - +
310A ARG* 3.9 21.5 - - - +
311A LEU 3.4 0.2 - - - -
312A ILE* 1.3 80.4 - - - +
314A MET* 1.3 58.3 + - - +
315A GLY 3.4 2.4 + - - -
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Residues in contact with MET 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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292A GLU* 6.2 4.7 - - + -
293A VAL* 4.0 14.1 - - - -
296A GLU* 3.6 14.1 - - - +
310A ARG* 3.3 52.9 + - - +
311A LEU* 3.0 13.9 + - - +
313A ASP* 1.3 74.9 - - - +
315A GLY* 1.3 61.5 + - - +
316A GLU* 3.3 18.1 + - + +
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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