Contacts of the helix formed by residues 308 - 318 (chain D) in PDB entry 2GL7
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 ASN 308 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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274D ARG* 3.4 29.2 + - - +
304D LEU 3.7 17.9 - - - +
305D ALA 3.2 3.9 + - - +
306D TYR 3.1 6.2 - - - +
307D GLY* 1.3 78.8 + - - +
309D GLN* 1.3 64.3 + - - +
310D GLU* 3.2 14.9 - - - +
311D SER* 2.9 42.0 + - - -
312D LYS* 3.2 16.8 + - - +
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Residues in contact with GLN 309 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307D GLY 4.0 2.2 + - - -
308D ASN* 1.3 71.8 - - - +
310D GLU* 1.3 63.4 + - - +
312D LYS* 3.2 14.7 + - + +
313D LEU* 3.1 40.3 + - + +
349D VAL* 5.0 0.9 - - - +
350D CYS* 3.3 46.3 + - - +
351D SER 5.7 0.2 - - - -
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Residues in contact with GLU 310 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A ARG* 4.3 29.2 + - - +
226A GLU* 5.5 5.8 - - - +
274D ARG* 6.1 1.7 - - - -
308D ASN* 3.2 10.0 - - - +
309D GLN* 1.3 78.5 - - - +
311D SER* 1.3 62.1 + - - +
313D LEU* 3.4 9.6 + - - +
314D ILE* 3.3 37.1 + - + +
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Residues in contact with SER 311 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274D ARG* 2.9 35.3 + - - -
279D LEU* 3.6 22.0 - - - +
304D LEU 3.4 17.7 + - - -
305D ALA* 4.1 7.0 - - - -
308D ASN* 2.9 12.7 + - - -
310D GLU* 1.3 75.4 - - - +
312D LYS* 1.3 64.9 + - - +
314D ILE* 3.3 3.3 + - - +
315D ILE* 3.1 29.3 + - - +
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Residues in contact with LYS 312 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305D ALA* 3.2 26.7 - - + +
307D GLY* 5.0 0.6 - - - -
308D ASN 3.2 18.7 + - - +
309D GLN* 3.2 32.1 + - - +
311D SER* 1.3 76.3 - - - +
313D LEU* 1.3 58.0 + - - +
315D ILE* 3.4 5.0 + - - +
316D LEU 3.0 17.7 + - - -
346D VAL* 2.9 24.8 + - + +
347D LEU* 3.9 18.6 - - + -
349D VAL* 3.5 10.9 - - - +
350D CYS* 3.9 9.0 - - + -
353D ASN* 3.0 28.3 + - - +
24E GLU* 2.6 30.5 + - - -
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Residues in contact with LEU 313 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309D GLN* 3.1 37.0 + - + +
310D GLU* 3.4 8.3 + - - +
311D SER 3.3 0.2 - - - -
312D LYS* 1.3 75.2 - - - +
314D ILE* 1.3 63.9 + - + +
316D LEU* 3.7 10.1 - - + +
317D ALA* 3.2 22.7 + - - +
350D CYS* 4.3 4.5 - - - -
352D SER* 3.9 30.1 - - - +
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Residues in contact with ILE 314 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274D ARG* 5.8 5.2 - - + +
279D LEU* 3.8 26.5 - - + -
280D GLN* 3.5 42.8 - - + +
310D GLU* 3.3 32.9 + - + +
311D SER* 3.3 5.8 + - - +
313D LEU* 1.3 74.8 - - + +
315D ILE* 1.3 62.4 + - - +
317D ALA* 3.3 5.8 + - - +
318D SER* 2.8 33.5 + - - +
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Residues in contact with ILE 315 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279D LEU* 4.3 23.6 - - + -
283D VAL* 4.3 21.5 - - + -
301D LEU* 4.3 16.6 - - + +
305D ALA* 3.8 27.1 - - + -
311D SER 3.1 21.1 + - - +
312D LYS* 3.6 4.9 - - - +
313D LEU 3.3 0.2 - - - -
314D ILE* 1.3 77.4 - - - +
316D LEU* 1.3 58.9 + - - +
318D SER* 3.3 7.6 + - - -
320D GLY* 2.9 41.2 + - - -
321D PRO* 4.7 0.4 - - + -
324D LEU* 5.2 3.4 - - + -
343D VAL* 5.2 3.8 - - + -
347D LEU* 3.9 26.9 - - + -
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Residues in contact with LEU 316 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312D LYS 3.0 13.8 + - - +
313D LEU* 3.7 12.3 - - + +
315D ILE* 1.3 78.0 - - - +
317D ALA* 1.3 63.1 + - - +
319D GLY* 3.3 13.0 + - - -
320D GLY 4.1 0.3 + - - -
321D PRO* 4.0 8.4 - - + +
352D SER* 3.5 40.2 - - - +
353D ASN* 3.4 21.3 - - - +
356D ALA* 3.7 28.9 - - + -
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Residues in contact with ALA 317 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313D LEU 3.2 14.5 + - - +
314D ILE* 3.8 6.5 - - - +
315D ILE 3.3 0.4 - - - -
316D LEU* 1.3 81.5 - - - +
318D SER* 1.3 59.0 + - - +
319D GLY 3.3 1.4 + - - -
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Residues in contact with SER 318 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280D GLN* 3.6 31.9 - - - +
283D VAL* 3.3 33.7 - - - +
284D ALA* 5.4 1.4 + - - -
314D ILE 2.8 22.6 + - - -
315D ILE* 3.3 2.3 + - - -
316D LEU 3.3 0.4 - - - -
317D ALA* 1.3 76.1 - - - +
319D GLY* 1.3 57.8 + - - +
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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