Contacts of the helix formed by residues 309 - 318 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B ILE* 3.6 18.6 - - + +
101B ILE* 3.6 20.9 - - + -
288B ILE* 3.7 21.8 - - + -
290B ILE* 3.4 39.9 - - + -
306B GLN* 4.3 10.6 + - - +
307B SER 2.7 3.6 + - - -
308B LYS* 1.3 79.3 - - + +
310B PHE* 1.3 76.1 + - - +
312B ASN* 3.3 3.6 + - - +
313B THR* 3.0 36.5 + - - -
333B LEU* 3.7 26.9 - - + -
423B LEU* 3.9 25.8 - - + -
426B TYR* 4.3 9.0 - + - -
428B MET* 5.8 0.4 - - - -
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Residues in contact with PHE 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306B GLN 5.2 0.6 + - - +
307B SER* 2.7 30.6 + - - +
309B PHE* 1.3 83.1 - - - +
311B GLU* 1.3 52.6 + - - +
312B ASN 2.6 14.2 + - - -
313B THR* 3.2 9.2 + - - -
314B VAL* 3.5 17.6 + - + +
328B LYS* 4.6 13.2 - - + -
330B ARG* 6.1 3.6 - - - -
333B LEU* 4.0 15.9 - - + +
426B TYR* 3.0 42.4 - + - +
310C PHE* 6.2 4.5 - + - -
328C LYS* 6.0 1.3 - - - -
330C ARG* 3.1 41.7 - - - -
310D PHE* 6.4 1.6 - + - -
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Residues in contact with GLU 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307B SER* 2.7 34.7 + - - +
308B LYS* 3.9 3.3 - - - +
310B PHE* 1.3 69.6 - - - +
312B ASN* 1.3 62.5 + - - +
314B VAL* 4.8 2.0 - - - -
315B ALA* 4.4 10.6 - - - +
330C ARG* 3.2 54.7 - - + +
331C LYS* 5.1 6.2 + - - +
333C LEU* 5.7 0.5 - - - +
334C TYR* 3.1 40.4 + - - +
426C TYR* 3.6 22.7 - - - +
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Residues in contact with ASN 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B ASN* 5.5 3.6 + - - +
78B ALA* 3.4 29.0 - - - +
86B ILE* 4.6 5.2 - - - -
88B PHE* 3.5 24.9 - - - -
308B LYS* 2.7 34.8 + - - +
309B PHE* 3.3 5.4 - - - +
310B PHE 2.6 8.9 + - - -
311B GLU* 1.3 72.1 + - - +
313B THR* 1.3 59.2 + - - +
314B VAL 2.9 3.6 - - - +
315B ALA* 3.5 12.0 - - - +
316B ASP* 2.8 28.9 + - - +
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Residues in contact with THR 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B PHE* 4.1 16.6 - - + -
99B PHE* 3.4 41.5 - - + -
288B ILE* 4.7 0.6 - - + +
309B PHE* 3.0 39.1 + - - -
310B PHE* 3.2 4.2 + - - -
312B ASN* 1.3 76.7 + - - +
314B VAL* 1.3 54.7 + - + +
316B ASP* 3.6 2.1 - - - +
317B ILE* 2.7 41.4 + - + +
332B ALA* 5.6 0.2 - - + -
333B LEU* 4.4 15.9 - - + -
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Residues in contact with VAL 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310B PHE* 3.5 20.9 - - + +
311B GLU* 4.8 0.9 - - - -
312B ASN 4.5 1.8 - - - +
313B THR* 1.3 78.7 - - - +
315B ALA* 1.3 55.4 + - - +
316B ASP 2.7 7.0 + - - -
317B ILE* 2.6 33.2 + - + -
318B MET* 2.8 14.6 + - + +
326B GLU 5.0 11.0 - - - +
328B LYS* 5.8 1.3 - - + +
333B LEU* 6.4 1.3 - - + -
328C LYS* 6.1 3.1 - - + -
330C ARG* 3.7 33.9 - - + +
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Residues in contact with ALA 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B ASN* 5.7 1.9 + - - -
63B ILE* 5.6 5.7 - - - +
311B GLU 4.4 4.4 - - - +
312B ASN* 3.3 20.5 + - - +
314B VAL* 1.3 78.4 - - - +
316B ASP* 1.3 57.7 + - - +
318B MET* 3.7 20.7 - - - +
319B SER* 4.5 6.4 + - - -
331C LYS* 3.4 29.4 - - - +
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Residues in contact with ASP 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B ASN* 3.5 14.2 + - - +
70B LEU* 4.3 21.3 - - - +
76B VAL* 3.5 26.6 - - - +
88B PHE* 4.0 27.2 - - + +
90B ILE* 5.0 4.7 - - - +
95B LEU* 5.4 8.0 - - - +
312B ASN* 2.8 18.4 + - - +
313B THR* 3.6 6.7 - - - +
314B VAL 2.7 1.4 + - - -
315B ALA* 1.3 77.5 - - - +
317B ILE* 1.3 60.8 + - - +
318B MET 3.0 5.2 - - - -
319B SER* 3.1 22.8 + - - -
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Residues in contact with ILE 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B LEU* 3.9 35.6 - - + +
313B THR* 2.7 32.2 + - + +
314B VAL* 2.6 19.4 + - + +
316B ASP* 1.3 72.1 - - - +
318B MET* 1.3 62.9 + - - +
319B SER 3.3 7.7 + - - +
325B ASP* 3.3 30.8 - - + +
326B GLU 4.6 9.9 - - - +
328B LYS 5.8 0.7 - - - +
329B LEU* 4.4 17.5 - - + -
332B ALA* 3.8 29.2 - - + -
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Residues in contact with MET 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B ILE* 4.6 16.8 - - + -
65B ALA* 5.2 11.4 - - + +
314B VAL* 2.8 13.8 + - + +
315B ALA* 3.7 15.5 - - - +
317B ILE* 1.3 79.2 - - - +
319B SER* 1.3 73.8 + - - +
325B ASP* 2.8 28.1 - - - +
326B GLU* 5.7 5.4 - - + +
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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