Contacts of the helix formed by residues 309 - 318 (chain P) 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 P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86P ILE* 3.6 19.0 - - + +
101P ILE* 3.6 20.6 - - + -
288P ILE* 3.7 22.9 - - + -
290P ILE* 3.4 38.8 - - + -
306P GLN* 4.3 11.2 + - - +
307P SER 2.8 0.8 + - - -
308P LYS* 1.3 83.5 - - + +
310P PHE* 1.3 74.9 + - - +
312P ASN* 3.3 3.0 + - - +
313P THR* 3.0 37.1 + - - -
333P LEU* 3.7 25.6 - - + -
423P LEU* 3.9 26.7 - - + -
426P TYR* 4.2 9.4 - + - -
428P MET* 5.7 0.7 - - - -
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Residues in contact with PHE 310 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310N PHE* 6.0 6.1 - + - -
328N LYS* 5.9 1.3 - - - -
330N ARG* 3.2 39.5 - - - -
310O PHE* 6.3 2.9 - + - -
306P GLN 5.2 0.6 + - - +
307P SER* 2.7 29.7 + - - +
309P PHE* 1.3 83.1 - - - +
311P GLU* 1.3 51.4 + - - +
312P ASN 2.6 14.4 + - - -
313P THR* 3.2 9.2 + - - -
314P VAL* 3.5 17.6 - - + +
328P LYS* 4.6 15.0 - - + -
330P ARG* 6.1 3.8 - - - -
333P LEU* 4.0 15.0 - - + -
426P TYR* 3.0 43.5 - + - +
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Residues in contact with GLU 311 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330N ARG* 3.0 55.7 - - + +
331N LYS* 5.1 4.7 + - - +
333N LEU* 5.5 0.7 - - - +
334N TYR* 3.2 39.2 + - - +
426N TYR* 3.7 23.7 - - - +
307P SER* 2.7 38.8 + - - +
308P LYS* 3.9 3.8 - - - +
310P PHE* 1.3 69.8 - - + +
312P ASN* 1.3 61.9 + - - +
314P VAL* 4.8 1.8 - - - -
315P ALA* 4.4 10.0 - - - +
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Residues in contact with ASN 312 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59P ASN* 5.5 3.8 + - - +
78P ALA* 3.4 28.2 - - - +
86P ILE* 4.6 5.2 - - - -
88P PHE* 3.5 24.9 - - + -
308P LYS* 2.7 35.7 + - - +
309P PHE* 3.3 5.4 - - - +
310P PHE 2.6 8.7 + - - -
311P GLU* 1.3 71.7 + - - +
313P THR* 1.3 59.8 + - - +
314P VAL 2.9 3.1 - - - +
315P ALA* 3.5 10.7 - - - +
316P ASP* 2.8 29.3 + - - +
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Residues in contact with THR 313 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88P PHE* 4.1 17.4 - - + -
99P PHE* 3.4 40.4 - - + -
288P ILE* 4.7 0.6 - - + +
309P PHE* 3.0 38.5 + - - -
310P PHE* 4.0 3.8 - - - -
312P ASN* 1.3 77.1 + - - +
314P VAL* 1.3 54.1 + - - +
316P ASP* 3.5 2.8 - - - +
317P ILE* 2.6 45.7 + - + +
332P ALA* 5.6 0.4 - - + -
333P LEU* 4.3 15.9 - - + -
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Residues in contact with VAL 314 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328N LYS* 5.8 3.8 - - + -
330N ARG* 3.5 38.6 - - + +
310P PHE* 3.5 19.5 - - + +
311P GLU* 4.8 0.4 - - - -
312P ASN 2.9 2.0 - - - +
313P THR* 1.3 77.5 - - + +
315P ALA* 1.3 54.9 + - - +
316P ASP 2.6 7.0 + - - -
317P ILE* 2.6 33.7 + - + -
318P MET* 2.8 14.1 + - + +
326P GLU 5.1 11.0 - - - +
328P LYS* 5.8 1.6 - - + +
333P LEU* 6.4 0.9 - - + -
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Residues in contact with ALA 315 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330N ARG* 6.2 1.9 - - + +
331N LYS* 3.3 30.5 - - - +
59P ASN* 5.7 1.8 + - - -
63P ILE* 5.5 6.1 - - - +
311P GLU 4.4 4.0 - - - +
312P ASN* 3.3 21.0 + - - +
314P VAL* 1.3 79.1 - - - +
316P ASP* 1.3 57.7 + - - +
318P MET* 3.7 21.0 - - - +
319P SER* 4.5 6.2 + - - -
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Residues in contact with ASP 316 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59P ASN* 3.5 14.3 + - - +
70P LEU* 4.3 21.5 - - - +
76P VAL* 3.5 27.0 - - - +
88P PHE* 4.0 26.1 - - + +
90P ILE* 5.0 4.5 - - - +
95P LEU* 5.5 7.4 - - - +
312P ASN* 2.8 18.1 + - - +
313P THR* 3.6 7.2 - - - +
314P VAL 2.6 1.0 + - - -
315P ALA* 1.3 77.3 - - - +
317P ILE* 1.3 63.7 + - - +
318P MET 3.0 1.6 - - - -
319P SER* 3.1 22.1 + - - -
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Residues in contact with ILE 317 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95P LEU* 3.9 36.7 - - + +
96P TYR 5.4 0.2 - - - +
99P PHE* 4.8 0.2 - - + -
313P THR* 2.6 32.9 + - + +
314P VAL* 2.6 22.9 + - + +
316P ASP* 1.3 72.1 - - - +
318P MET* 1.3 61.4 + - - +
319P SER 3.3 7.0 + - - +
325P ASP* 3.3 31.1 - - + +
326P GLU* 4.5 9.0 - - - +
328P LYS 5.7 0.7 - - - +
329P LEU* 4.4 17.3 - - + -
332P ALA* 3.8 28.5 - - + -
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Residues in contact with MET 318 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63P ILE* 4.6 16.2 - - + -
65P ALA* 5.2 10.3 - - + +
314P VAL* 2.8 15.3 + - + +
315P ALA* 3.7 15.0 - - - +
316P ASP 3.0 0.2 - - - -
317P ILE* 1.3 79.0 - - - +
319P SER* 1.3 73.4 + - - +
325P ASP* 2.8 28.1 - - - +
326P 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