Contacts of the helix formed by residues 299 - 308 (chain Q) in PDB entry 5GJQ
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 299 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297Q ARG 4.2 0.4 + - - -
298Q SER* 1.3 72.7 - - - +
300Q ALA* 1.3 68.5 + - - +
301Q ASP 3.1 1.3 - - - -
302Q PHE* 3.2 7.6 + - + +
303Q GLU* 2.8 35.6 + - + +
327Q TYR* 3.4 45.8 - - + +
330Q LEU* 4.2 5.8 - - + +
331Q LEU* 3.4 50.9 - - + +
334Q ASN* 4.3 3.2 - - - +
354Q ILE* 3.6 33.9 - - + +
356Q LEU* 5.8 0.9 - - + -
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Residues in contact with ALA 300 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298Q SER* 4.3 3.1 + - - +
299Q LEU* 1.3 78.6 - - - +
301Q ASP* 1.3 60.5 + - - +
303Q GLU* 3.4 9.5 + - - +
304Q LYS* 3.1 20.6 + - - +
354Q ILE* 5.5 2.0 + - - +
355Q LYS* 6.4 2.0 - - + -
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Residues in contact with ASP 301 (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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289Q CYS* 4.1 2.9 - - - +
293Q ALA* 2.6 39.2 - - + +
296Q ASN* 4.2 9.3 + - - +
298Q SER* 2.8 22.7 + - - +
299Q LEU 3.1 0.8 - - - -
300Q ALA* 1.3 74.8 - - - +
302Q PHE* 1.3 62.7 + - - +
304Q LYS* 2.4 41.1 + - - +
305Q ALA* 3.0 6.8 + - - +
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Residues in contact with PHE 302 (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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290Q VAL* 3.6 37.7 - - + -
293Q ALA* 4.5 4.0 - - + +
298Q SER 4.0 2.5 + - - +
299Q LEU* 3.2 11.0 + - + +
301Q ASP* 1.3 80.0 - - - +
303Q GLU* 1.3 53.1 + - + +
305Q ALA* 3.2 7.4 + - + +
306Q LEU* 2.8 68.0 + - + +
323Q LEU* 4.0 23.1 - - + -
326Q LEU* 3.4 28.7 - - + -
327Q TYR* 3.5 33.7 - + + -
330Q LEU* 2.5 34.8 - - + -
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Residues in contact with GLU 303 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299Q LEU* 2.8 33.2 + - + +
300Q ALA* 3.5 9.9 - - - +
302Q PHE* 1.3 78.0 - - + +
304Q LYS* 1.3 50.5 + - - +
306Q LEU* 3.1 19.3 + - + +
307Q THR* 2.8 33.7 + - - -
327Q TYR* 5.8 3.6 - - + -
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Residues in contact with LYS 304 (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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300Q ALA 3.1 7.8 + - - +
301Q ASP* 2.4 53.8 + - - +
303Q GLU* 1.3 75.2 - - - +
305Q ALA* 1.3 59.5 + - + +
307Q THR* 3.0 11.0 + - - -
308Q ASP* 2.9 36.0 + - - -
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Residues in contact with ALA 305 (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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289Q CYS* 5.3 4.7 - - + -
290Q VAL* 3.8 32.7 - - + +
301Q ASP* 3.0 14.5 + - - +
302Q PHE* 3.5 10.5 - - + +
304Q LYS* 1.3 74.4 - - + +
306Q LEU* 1.3 62.6 + - - +
307Q THR 3.2 0.9 - - - -
308Q ASP* 4.3 9.6 - - - -
309Q TYR* 3.8 20.9 + - + +
313Q LEU* 3.6 19.6 - - - +
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Residues in contact with LEU 306 (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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302Q PHE* 2.8 46.7 + - + +
303Q GLU* 3.1 21.7 + - + +
305Q ALA* 1.3 78.1 - - - +
307Q THR* 1.3 57.4 + - - +
310Q ARG* 3.2 25.7 - - - +
313Q LEU* 4.8 4.9 - - + -
323Q LEU* 3.6 45.1 - - + +
327Q TYR* 5.4 6.3 - - + -
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Residues in contact with THR 307 (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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303Q GLU 2.8 19.1 + - - -
304Q LYS* 3.0 13.5 + - - -
306Q LEU* 1.3 76.9 - - - +
308Q ASP* 1.3 61.7 + - - +
310Q ARG* 3.1 25.3 - - - +
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Residues in contact with ASP 308 (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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282Q ARG* 5.4 3.8 + - - -
304Q LYS* 2.9 27.1 + - - +
305Q ALA* 4.3 1.1 - - - -
307Q THR* 1.3 74.3 - - - +
309Q TYR* 1.3 87.4 + - + +
310Q ARG* 3.3 1.5 + - - +
311Q ALA* 4.4 9.5 + - - +
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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