Contacts of the helix formed by residues 331 - 344 (chain D) in PDB entry 6GL7
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 MET 331 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252D LEU* 3.4 29.4 - - + -
255D ARG* 6.2 0.4 - - - +
328D SER* 3.0 16.5 + - - +
329D GLY 2.9 0.2 + - - -
330D ASN* 1.3 87.7 - - + +
332D GLU* 1.3 61.7 + - - +
333D GLU 3.2 3.1 - - - -
334D GLU* 3.2 41.4 + - + +
335D CYS* 3.0 22.0 + - - +
263E TYR* 5.9 1.6 - - - -
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Residues in contact with GLU 332 (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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325D CYS* 4.7 9.1 - - + +
328D SER* 3.6 13.6 - - - -
329D GLY* 3.0 41.3 + - - +
330D ASN 3.5 1.0 - - - -
331D MET* 1.3 76.8 - - - +
333D GLU* 1.3 63.0 + - - +
335D CYS* 3.4 2.0 + - - +
336D GLU* 3.0 34.6 + - + +
235E GLU 5.2 4.2 - - - +
236E LYS* 4.9 13.7 + - - -
261E THR* 6.2 3.1 - - + +
305E PRO 4.5 3.6 - - - +
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Residues in contact with GLU 333 (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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330D ASN 5.0 0.8 + - - +
331D MET 3.2 0.6 - - - -
332D GLU* 1.3 78.1 - - - +
334D GLU* 1.3 58.5 + - - +
336D GLU* 3.2 8.5 + - - +
337D LYS* 2.5 47.2 + - + +
173E SER* 2.8 29.4 + - - -
175E ARG* 3.0 39.8 + - - +
261E THR* 3.0 26.5 + - + +
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Residues in contact with GLU 334 (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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122D PHE* 3.6 27.1 - - + -
252D LEU* 4.6 8.8 - - + +
255D ARG* 5.8 0.4 + - - +
330D ASN 4.0 1.9 - - - +
331D MET* 3.2 53.4 + - + +
333D GLU* 1.3 77.1 - - + +
335D CYS* 1.3 63.1 + - - +
337D LYS* 3.2 14.0 + - + +
338D PHE* 3.1 19.6 + - - +
34E ASP* 4.6 3.1 - - - +
175E ARG* 3.1 34.9 + - - +
263E TYR* 4.9 0.2 + - - -
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Residues in contact with CYS 335 (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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250D ASN* 3.6 13.9 - - - -
251D CYS* 3.8 18.4 - - - +
252D LEU* 4.0 16.4 - - + +
325D CYS* 2.1 51.6 - - + -
328D SER* 3.6 14.6 - - - +
331D MET 3.0 9.0 + - - +
332D GLU 3.6 6.3 - - - +
334D GLU* 1.3 78.6 - - - +
336D GLU* 1.3 57.4 + - - +
338D PHE* 3.3 3.4 + - - +
339D LEU* 3.0 26.2 + - - +
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Residues in contact with GLU 336 (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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325D CYS* 4.0 16.3 - - + +
332D GLU* 3.0 24.8 + - - +
333D GLU* 3.8 5.3 - - - +
335D CYS* 1.3 74.0 - - - +
337D LYS* 1.3 62.3 + - - +
338D PHE 3.0 0.5 + - - -
339D LEU* 4.2 8.7 - - + -
340D ARG* 2.6 74.7 + - + +
236E LYS* 5.4 5.9 + - - -
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Residues in contact with LYS 337 (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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122D PHE* 3.7 36.3 - - + +
123D TYR* 4.0 16.9 + - - +
333D GLU* 2.5 32.5 + - + +
334D GLU* 3.2 14.5 + - + +
336D GLU* 1.3 73.2 - - - +
338D PHE* 1.3 59.2 + - - +
340D ARG* 4.2 9.7 + - - +
341D ASP* 3.7 19.1 + - - +
34E ASP* 5.8 2.2 + - - -
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Residues in contact with PHE 338 (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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122D PHE* 3.8 19.5 - + + -
123D TYR* 4.9 8.7 - + - -
251D CYS* 5.0 9.6 - - + -
255D ARG* 3.9 25.8 - - + +
268D LEU* 3.7 36.6 - - + -
271D PHE* 4.4 13.2 - + - -
272D HIS* 5.1 4.5 - + + -
305D MET* 3.9 25.4 - - + -
321D PRO* 5.5 1.1 - - + -
334D GLU 3.1 7.1 + - - +
335D CYS* 3.9 5.8 - - - +
336D GLU 3.1 0.2 - - - -
337D LYS* 1.3 75.0 - - - +
339D LEU* 1.3 67.3 + - + +
340D ARG 3.2 1.3 - - - -
341D ASP* 3.0 31.8 + - - +
342D PHE* 3.5 37.1 - + - -
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Residues in contact with LEU 339 (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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251D CYS* 3.8 31.9 - - + -
320D SER* 4.1 13.0 - - - -
321D PRO* 3.9 26.5 - - + +
323D CYS* 4.6 7.6 - - - +
324D SER* 5.0 3.1 - - - -
325D CYS* 4.2 14.8 - - - -
335D CYS 3.0 18.9 + - - +
336D GLU* 3.9 7.2 - - + +
338D PHE* 1.3 78.6 - - + +
340D ARG* 1.3 63.0 + - - +
342D PHE* 3.0 23.1 + - - +
343D THR* 3.7 10.4 + - + +
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Residues in contact with ARG 340 (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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277D ALA* 6.3 0.2 - - - -
336D GLU* 2.6 63.5 + - + +
337D LYS* 4.3 8.7 - - - +
339D LEU* 1.3 71.8 - - - +
341D ASP* 1.3 59.2 + - - +
342D PHE 3.0 2.5 + - - -
343D THR* 4.2 8.1 - - - +
344D GLU* 2.7 86.1 + - + +
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Residues in contact with ASP 341 (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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123D TYR* 3.1 32.9 + - - -
271D PHE* 3.6 19.4 - - + -
272D HIS* 4.7 4.0 - - - +
275D CYS 4.9 2.5 - - - +
276D ARG* 4.8 5.1 - - - +
277D ALA* 4.1 22.4 + - - +
337D LYS 3.7 11.8 - - - +
338D PHE* 3.0 20.2 + - + +
340D ARG* 1.3 77.5 - - - +
342D PHE* 1.3 56.6 + - - +
345D ASN* 3.0 32.0 + - - +
348D LEU* 3.4 5.2 - - - +
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Residues in contact with PHE 342 (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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271D PHE* 3.5 33.7 - + - -
297D TYR* 4.7 5.2 - + - -
300D MET* 5.9 3.8 - - + -
305D MET* 4.5 8.3 - - + -
307D PRO* 4.1 25.8 - - + -
318D VAL* 5.4 0.2 - - - -
319D VAL* 3.1 35.6 + - + +
320D SER* 3.8 7.4 - - - -
321D PRO* 3.6 30.5 - - + -
338D PHE* 3.5 50.7 - + - -
339D LEU* 3.0 17.9 + - - +
341D ASP* 1.3 80.3 - - - +
343D THR* 1.3 58.9 + - - +
344D GLU 3.8 0.2 - - - -
345D ASN* 4.6 2.3 + - - +
348D LEU* 3.6 12.7 - - + +
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Residues in contact with THR 343 (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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310D VAL* 4.9 2.0 - - + -
318D VAL* 3.7 26.0 - - + +
319D VAL 3.1 18.8 - - - +
320D SER* 3.7 17.0 - - - +
339D LEU* 3.7 14.9 + - + +
340D ARG* 3.2 3.3 + - - +
342D PHE* 1.3 77.0 - - + +
344D GLU* 1.3 72.0 + - - +
345D ASN 3.4 5.6 + - - -
349D ARG* 3.7 22.0 + - - -
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Residues in contact with GLU 344 (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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277D ALA* 4.6 4.9 - - - +
340D ARG* 2.7 65.0 + - + +
343D THR* 1.3 81.8 + - - +
345D ASN* 1.3 57.2 + - - +
346D PRO* 3.4 11.4 - - - +
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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