Contacts of the helix formed by residues 309 - 318 (chain Q) in PDB entry 2GLJ
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 PHE 309 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86Q ILE* 3.6 17.7 - - + +
101Q ILE* 3.6 20.4 - - + -
288Q ILE* 3.8 22.4 - - + -
290Q ILE* 3.4 38.1 - - + -
306Q GLN* 4.2 10.1 + - - +
307Q SER 2.7 4.4 + - - -
308Q LYS* 1.3 79.3 - - + +
310Q PHE* 1.3 75.4 + - - +
312Q ASN* 3.3 3.7 + - - +
313Q THR* 3.0 36.5 + - - -
333Q LEU* 3.7 25.8 - - + -
423Q LEU* 3.9 25.6 - - + -
426Q TYR* 4.2 9.9 - + - -
428Q MET* 5.6 0.9 - - - -
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Residues in contact with PHE 310 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310M PHE* 6.2 4.9 - + - -
306Q GLN 5.1 0.6 + - - +
307Q SER* 2.7 30.6 + - - +
309Q PHE* 1.3 83.3 - - - +
311Q GLU* 1.3 51.7 + - - +
312Q ASN 2.6 14.2 + - - -
313Q THR* 3.2 8.8 + - - -
314Q VAL* 3.5 18.4 + - + +
328Q LYS* 4.6 15.5 - - + -
330Q ARG* 6.1 4.0 - - - -
333Q LEU* 4.0 14.8 - - + -
426Q TYR* 3.0 42.8 - + - +
310U PHE* 6.2 4.0 - + - -
328U LYS* 5.9 1.6 - - - -
330U ARG* 3.3 38.1 - - - -
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Residues in contact with GLU 311 (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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307Q SER* 2.7 33.9 + - - +
308Q LYS* 3.9 4.2 - - - +
310Q PHE* 1.3 70.0 - - - +
312Q ASN* 1.3 62.7 + - - +
314Q VAL* 4.8 2.2 - - - -
315Q ALA* 4.4 10.9 - - - +
330U ARG* 3.0 56.8 - - + +
331U LYS* 5.3 4.2 + - - +
333U LEU* 5.8 0.9 - - - +
334U TYR* 3.4 35.3 + - - +
426U TYR* 3.8 21.7 - - - +
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Residues in contact with ASN 312 (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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59Q ASN* 5.5 4.0 + - - +
78Q ALA* 3.4 29.2 - - - +
86Q ILE* 4.6 5.6 - - - -
88Q PHE* 3.4 24.8 - - - -
308Q LYS* 2.8 34.1 + - - +
309Q PHE* 3.4 5.2 - - - +
310Q PHE 2.6 8.3 + - - -
311Q GLU* 1.3 73.8 + - - +
313Q THR* 1.3 59.4 + - - +
314Q VAL 2.9 2.7 - - - +
315Q ALA* 3.6 10.9 - - - +
316Q ASP* 2.8 29.3 + - - +
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Residues in contact with THR 313 (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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88Q PHE* 4.1 17.2 - - + -
99Q PHE* 3.3 42.2 - - + -
288Q ILE* 5.1 0.4 - - + -
309Q PHE* 3.0 39.5 + - - -
310Q PHE* 3.2 3.8 + - - -
312Q ASN* 1.3 77.0 + - - +
314Q VAL* 1.3 55.6 + - + +
316Q ASP* 3.4 2.9 + - - +
317Q ILE* 2.7 41.1 + - + +
332Q ALA* 5.6 0.4 - - + -
333Q LEU* 4.4 15.0 - - + -
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Residues in contact with VAL 314 (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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310Q PHE* 3.5 20.9 - - + +
311Q GLU* 4.8 0.7 - - - -
312Q ASN 2.9 1.5 - - - +
313Q THR* 1.3 78.3 - - + +
315Q ALA* 1.3 56.5 + - - +
316Q ASP 2.6 7.5 + - - -
317Q ILE* 2.6 33.6 + - + -
318Q MET* 2.8 14.6 + - + +
326Q GLU 5.1 10.8 - - - +
328Q LYS* 5.8 1.6 - - + +
333Q LEU* 6.4 1.1 - - + -
328U LYS* 6.0 2.9 - - + -
330U ARG* 3.7 35.0 - - + +
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Residues in contact with ALA 315 (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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59Q ASN* 5.7 1.6 + - - -
63Q ILE* 5.6 5.7 - - - +
311Q GLU 4.4 4.9 - - - +
312Q ASN* 3.3 21.0 + - - +
314Q VAL* 1.3 78.9 - - - +
316Q ASP* 1.3 58.5 + - - +
318Q MET* 3.7 21.7 - - - +
319Q SER* 4.4 5.9 + - - -
331U LYS* 3.6 27.8 - - - +
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Residues in contact with ASP 316 (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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59Q ASN* 3.5 13.6 + - - +
70Q LEU* 4.2 20.7 - - - +
76Q VAL* 3.5 27.0 - - - +
88Q PHE* 4.0 26.1 - - + +
90Q ILE* 5.0 4.5 - - - +
95Q LEU* 5.5 8.0 - - - +
312Q ASN* 2.8 18.1 + - - +
313Q THR* 3.5 8.1 - - - +
314Q VAL 2.6 1.4 + - - -
315Q ALA* 1.3 78.4 - - - +
317Q ILE* 1.3 59.8 + - - +
318Q MET 3.0 5.2 - - - -
319Q SER* 3.2 22.1 + - - -
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Residues in contact with ILE 317 (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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95Q LEU* 3.9 35.7 - - + +
96Q TYR 5.3 0.4 - - - +
99Q PHE* 4.8 0.2 - - + -
313Q THR* 2.7 31.3 + - + +
314Q VAL* 2.6 21.4 + - + +
316Q ASP* 1.3 69.8 - - - +
318Q MET* 1.3 63.5 + - - +
319Q SER 3.3 5.0 + - - +
325Q ASP* 3.2 32.7 - - + +
326Q GLU 4.5 9.9 - - - +
328Q LYS 5.7 0.7 - - - +
329Q LEU* 4.4 17.7 - - + -
332Q ALA* 3.8 28.9 - - + -
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Residues in contact with MET 318 (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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63Q ILE* 4.6 17.0 - - + -
65Q ALA* 5.2 10.5 - - + +
314Q VAL* 2.8 10.2 + - + +
315Q ALA* 3.7 19.3 - - - +
316Q ASP 3.0 0.2 - - - -
317Q ILE* 1.3 80.1 - - - +
319Q SER* 1.3 73.1 + - - +
325Q ASP* 2.8 28.2 - - - +
326Q GLU* 5.7 5.6 - - + +
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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