Contacts of the helix formed by residues 309 - 318 (chain M) 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 M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86M ILE* 3.6 18.3 - - + +
101M ILE* 3.6 20.9 - - + -
288M ILE* 3.8 22.4 - - + -
290M ILE* 3.4 38.1 - - + -
306M GLN* 4.2 10.3 + - - +
307M SER 2.8 1.6 + - - -
308M LYS* 1.3 82.8 - - + +
310M PHE* 1.3 73.9 + - - +
312M ASN* 3.3 3.0 + - - +
313M THR* 3.0 36.3 + - - -
333M LEU* 3.7 26.0 - - + -
423M LEU* 3.9 24.9 - - + -
426M TYR* 4.3 9.4 - + - -
428M MET* 5.7 0.4 - - - -
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Residues in contact with PHE 310 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306M GLN 5.1 0.6 + - - +
307M SER* 2.7 30.0 + - - +
309M PHE* 1.3 84.2 - - - +
311M GLU* 1.3 51.5 + - - +
312M ASN 2.6 14.4 + - - -
313M THR* 3.2 8.4 + - - -
314M VAL* 3.5 18.9 + - + +
328M LYS* 4.6 14.6 - - + -
330M ARG* 6.1 3.6 - - - -
333M LEU* 4.0 14.8 - - + +
426M TYR* 3.1 43.7 - + - +
310Q PHE* 6.2 4.3 - + - -
328Q LYS* 5.9 1.3 - - - -
330Q ARG* 3.1 41.5 - - - -
310U PHE* 6.4 2.0 - + - -
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Residues in contact with GLU 311 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307M SER* 2.6 39.8 + - - +
308M LYS* 3.9 3.6 - - - +
310M PHE* 1.3 69.0 - - - +
312M ASN* 1.3 62.3 + - - +
314M VAL* 4.8 2.0 - - - -
315M ALA* 4.4 10.9 - - - +
330Q ARG* 3.1 56.9 - - + +
331Q LYS* 5.1 5.9 + - - +
333Q LEU* 5.7 0.5 - - - +
334Q TYR* 3.2 39.9 + - - +
426Q TYR* 3.8 21.4 - - - +
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Residues in contact with ASN 312 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59M ASN* 5.4 4.0 + - - +
78M ALA* 3.4 28.2 - - - +
86M ILE* 4.6 4.5 - - + -
88M PHE* 3.5 24.9 - - + -
308M LYS* 2.7 36.3 + - - +
309M PHE* 3.3 4.3 - - - +
310M PHE 2.6 9.3 + - - -
311M GLU* 1.3 73.0 + - - +
313M THR* 1.3 59.5 + - - +
314M VAL 2.9 3.5 - - - +
315M ALA* 3.5 11.2 - - - +
316M ASP* 2.8 28.8 + - - +
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Residues in contact with THR 313 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88M PHE* 4.1 17.2 - - + -
99M PHE* 3.4 40.6 - - + -
288M ILE* 4.7 0.8 - - + +
309M PHE* 3.0 38.7 + - - -
310M PHE* 4.0 4.0 - - - -
312M ASN* 1.3 76.4 + - - +
314M VAL* 1.3 54.5 + - + +
316M ASP* 3.5 2.8 - - - +
317M ILE* 2.7 41.1 + - + +
332M ALA* 5.6 0.4 - - + -
333M LEU* 4.4 15.9 - - + -
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Residues in contact with VAL 314 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310M PHE* 3.5 20.6 - - + +
311M GLU* 4.8 1.1 - - - -
312M ASN 4.5 1.3 - - - +
313M THR* 1.3 78.3 - - - +
315M ALA* 1.3 56.2 + - - +
316M ASP 2.7 6.8 + - - -
317M ILE* 2.6 33.1 + - + -
318M MET* 2.7 14.9 + - + +
326M GLU 5.0 11.0 - - - +
328M LYS* 5.8 1.3 - - + +
333M LEU* 6.4 1.1 - - + -
328Q LYS* 6.0 3.4 - - + -
330Q ARG* 3.6 34.8 - - + +
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Residues in contact with ALA 315 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59M ASN* 5.7 1.8 + - - -
63M ILE* 5.6 6.2 - - - +
311M GLU 4.4 4.6 - - - +
312M ASN* 3.3 21.2 + - - +
314M VAL* 1.3 79.9 - - - +
316M ASP* 1.3 57.8 + - - +
318M MET* 3.7 20.9 - - - +
319M SER* 4.4 5.9 + - - -
331Q LYS* 3.4 30.1 - - - +
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Residues in contact with ASP 316 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59M ASN* 3.5 14.6 + - - +
70M LEU* 4.3 20.6 - - - +
76M VAL* 3.5 26.8 - - - +
88M PHE* 4.0 27.5 - - + +
90M ILE* 5.0 4.7 - - - +
95M LEU* 5.5 8.0 - - - +
312M ASN* 2.8 18.2 + - - +
313M THR* 3.5 7.2 - - - +
314M VAL 2.7 1.4 + - - -
315M ALA* 1.3 78.5 - - - +
317M ILE* 1.3 63.6 + - - +
318M MET 3.0 1.8 - - - -
319M SER* 3.1 22.0 + - - -
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Residues in contact with ILE 317 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95M LEU* 3.9 36.3 - - + +
99M PHE* 4.7 0.2 - - + -
313M THR* 2.7 33.1 + - + +
314M VAL* 2.6 20.7 + - + +
316M ASP* 1.3 72.5 - - - +
318M MET* 1.3 63.1 - - - +
319M SER 3.3 4.7 + - - +
325M ASP* 3.3 32.2 - - + +
326M GLU 4.5 9.9 - - - +
328M LYS 5.9 0.2 - - - +
329M LEU* 4.5 18.2 - - + -
332M ALA* 3.8 27.8 - - + -
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Residues in contact with MET 318 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63M ILE* 4.7 16.4 - - + -
65M ALA* 5.2 11.0 - - + -
314M VAL* 2.7 11.2 + - + +
315M ALA* 3.7 19.1 - - - +
316M ASP 3.0 0.2 - - - -
317M ILE* 1.3 78.4 - - - +
319M SER* 1.3 72.4 + - - +
325M ASP* 2.8 29.6 - - - +
326M 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