Contacts of the helix formed by residues 309 - 318 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86C ILE* 3.6 18.6 - - + +
101C ILE* 3.6 26.2 - - + -
288C ILE* 3.8 16.8 - - + -
290C ILE* 3.4 39.9 - - + -
306C GLN* 4.2 10.3 + - - +
307C SER 2.8 0.8 + - - -
308C LYS* 1.3 83.2 - - + +
310C PHE* 1.3 74.6 + - - +
312C ASN* 3.3 3.1 + - - +
313C THR* 3.0 37.3 + - - -
333C LEU* 3.7 26.0 - - + -
423C LEU* 3.9 26.5 - - + -
426C TYR* 4.2 8.7 - + - -
428C MET* 5.7 0.9 - - - -
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Residues in contact with PHE 310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B PHE* 6.2 3.8 - + - -
306C GLN 5.2 0.6 + - - +
307C SER* 2.7 29.2 + - - +
309C PHE* 1.3 83.5 - - - +
311C GLU* 1.3 51.3 + - - +
312C ASN 2.6 14.6 + - - -
313C THR* 3.2 9.0 + - - -
314C VAL* 3.5 18.4 + - + +
328C LYS* 4.6 14.6 - - + -
330C ARG* 6.2 3.8 - - - -
333C LEU* 4.0 15.9 - - + +
426C TYR* 3.0 43.3 - + - +
310D PHE* 6.2 3.4 - + - -
328D LYS* 5.8 1.8 - - - -
330D ARG* 3.1 40.8 - - - -
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Residues in contact with GLU 311 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307C SER* 2.6 39.6 + - - +
308C LYS* 4.0 3.8 - - - +
310C PHE* 1.3 69.6 - - - +
312C ASN* 1.3 62.3 + - - +
314C VAL* 4.8 2.5 - - - -
315C ALA* 4.4 10.8 - - - +
330D ARG* 3.0 58.5 - - + +
331D LYS* 5.1 6.8 + - - +
333D LEU* 5.9 0.7 - - - +
334D TYR* 3.4 35.7 + - - +
426D TYR* 4.0 20.1 - - - +
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Residues in contact with ASN 312 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C ASN* 5.5 3.2 + - - +
78C ALA* 3.4 28.4 - - - +
86C ILE* 4.6 4.5 - - - -
88C PHE* 3.4 25.8 - - + -
308C LYS* 2.7 35.5 + - - +
309C PHE* 3.3 5.4 - - - +
310C PHE 2.6 8.3 + - - -
311C GLU* 1.3 73.6 + - - +
313C THR* 1.3 59.9 + - - +
314C VAL 2.9 2.9 - - - +
315C ALA* 3.5 12.5 - - - +
316C ASP* 2.7 29.3 + - - +
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Residues in contact with THR 313 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C PHE* 4.1 16.8 - - + -
99C PHE* 3.3 41.3 - - + -
288C ILE* 4.7 1.0 - - + +
309C PHE* 3.0 38.7 + - - -
310C PHE* 4.0 3.8 - - - -
312C ASN* 1.3 77.3 - - - +
314C VAL* 1.3 54.6 + - + +
316C ASP* 3.4 3.0 + - - +
317C ILE* 2.6 41.9 + - + +
332C ALA* 5.6 0.4 - - + -
333C LEU* 4.4 15.5 - - + -
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Residues in contact with VAL 314 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310C PHE* 3.5 21.7 + - + +
311C GLU* 4.8 1.1 - - - -
312C ASN 4.5 1.6 - - - +
313C THR* 1.3 77.5 - - - +
315C ALA* 1.3 56.9 + - - +
316C ASP 2.6 15.2 + - - -
317C ILE* 2.6 25.6 + - + -
318C MET* 2.7 14.4 + - + +
326C GLU 5.0 11.0 - - - +
328C LYS* 5.7 2.2 - - + +
333C LEU* 6.4 0.7 - - + -
328D LYS* 6.1 3.1 - - + -
330D ARG* 3.7 32.8 - - + +
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Residues in contact with ALA 315 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C ASN* 5.7 1.8 + - - -
63C ILE* 5.6 5.9 - - - +
311C GLU 4.4 4.4 - - - +
312C ASN* 3.3 20.7 + - - +
314C VAL* 1.3 78.3 - - - +
316C ASP* 1.3 58.5 + - - +
318C MET* 3.7 21.3 - - - +
319C SER* 4.5 6.2 + - - -
331D LYS* 3.5 28.0 - - - +
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Residues in contact with ASP 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C ASN* 3.5 14.6 + - - +
70C LEU* 4.3 21.0 - - - +
76C VAL* 3.5 27.1 - - - +
88C PHE* 4.0 26.1 - - + -
90C ILE* 5.0 5.2 - - - +
95C LEU* 5.5 8.3 - - - +
312C ASN* 2.7 19.2 + - - +
313C THR* 3.5 6.7 - - - +
314C VAL 2.6 1.4 + - - -
315C ALA* 1.3 78.3 - - - +
317C ILE* 1.3 64.2 + - - +
318C MET 3.0 2.0 - - - -
319C SER* 3.2 21.1 + - - -
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Residues in contact with ILE 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C LEU* 3.9 36.8 - - + +
99C PHE* 4.9 0.2 - - + -
313C THR* 2.6 34.5 + - + +
314C VAL* 2.6 17.1 + - + +
316C ASP* 1.3 72.3 - - - +
318C MET* 1.3 64.3 + - - +
319C SER 3.3 7.5 + - - +
325C ASP* 3.3 31.0 - - - +
326C GLU* 4.5 9.6 - - - +
328C LYS 5.8 0.2 - - - +
329C LEU* 4.4 18.2 - - + -
332C ALA* 3.8 28.5 - - + -
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Residues in contact with MET 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C ILE* 4.7 16.2 - - + -
65C ALA* 5.2 10.5 - - + +
314C VAL* 2.7 14.6 + - + +
315C ALA* 3.7 14.4 - - - +
316C ASP 3.0 0.4 - - - -
317C ILE* 1.3 78.4 - - - +
319C SER* 1.3 74.1 + - - +
325C ASP* 2.9 28.3 - - - +
326C 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