Contacts of the helix formed by residues 1327 - 1338 (chain D) in PDB entry 6PB4
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 GLU1327 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92 C 3.7 20.8 - - - +
102 A 3.3 8.1 + - - -
120D LEU* 6.1 1.4 - - - +
1314D LEU* 4.5 13.7 - - + -
1326D GLN* 1.3 99.9 + - - +
1328D THR* 1.3 64.8 + - - +
1329D THR 3.6 1.1 - - - -
1330D ARG* 2.8 46.0 + - + +
1331D VAL* 3.2 21.8 + - + +
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Residues in contact with THR1328 (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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331D ILE* 4.8 18.7 + - + +
332D LYS* 6.0 2.5 - - - -
338D PHE* 5.3 0.4 - - + -
1323D ALA* 2.9 34.7 + - + +
1324D SER 4.1 1.2 + - - -
1325D PHE 3.8 3.1 + - - -
1326D GLN* 3.5 20.0 + - - -
1327D GLU* 1.3 74.0 - - - +
1329D THR* 1.3 68.3 + - - +
1331D VAL* 2.9 19.0 + - - +
1332D LEU* 2.9 37.4 + - + +
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Residues in contact with THR1329 (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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115D TRP* 3.4 51.8 - - + +
119D SER* 6.1 0.2 - - - -
308D ASP* 5.9 0.7 - - - +
311D ARG* 6.1 0.2 - - - +
328D ALA* 5.4 0.7 - - - +
332D LYS* 3.9 19.9 + - - -
1328D THR* 1.3 77.0 - - - +
1330D ARG* 1.3 81.5 + - - +
1332D LEU* 3.2 13.7 + - - +
1333D THR* 3.0 33.9 + - + +
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Residues in contact with ARG1330 (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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82 T 3.8 8.1 + - - -
92 C 2.7 27.9 + - - -
115D TRP* 6.2 0.2 - - - +
119D SER* 3.1 46.6 + - - +
120D LEU* 5.3 4.4 - - + +
123D ARG* 5.3 5.4 + - - +
311D ARG* 3.6 26.6 - - - +
1327D GLU* 2.8 49.2 + - + +
1328D THR 3.0 0.4 + - - -
1329D THR* 1.3 94.3 - - - +
1331D VAL* 1.3 66.1 + - + +
1333D THR* 2.3 25.6 + - - -
1334D GLU* 2.9 12.7 + - - +
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Residues in contact with VAL1331 (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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1314D LEU* 4.3 26.2 - - + +
1319D PHE* 4.0 28.3 - - + +
1322D ALA* 4.1 20.6 - - + +
1323D ALA* 4.6 2.9 - - + +
1327D GLU* 3.2 20.6 - - + +
1328D THR* 2.9 8.4 + - - +
1330D ARG* 1.3 76.6 - - + +
1332D LEU* 1.3 59.1 + - + +
1334D GLU* 3.4 9.5 + - - +
1335D ALA* 2.8 27.4 + - - +
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Residues in contact with LEU1332 (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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1330C ILE* 5.5 14.8 - - + -
22D ILE* 4.8 4.0 - - + +
115D TRP* 4.7 16.2 - - + -
331D ILE* 5.5 6.3 - - + -
338D PHE* 6.5 0.2 - - + -
1319D PHE* 4.6 15.7 - - + -
1323D ALA* 3.8 24.7 - - + -
1328D THR* 2.9 40.8 + - + +
1329D THR* 3.4 11.4 - - - +
1331D VAL* 1.3 74.5 - - - +
1333D THR* 1.3 60.6 + - - +
1335D ALA* 3.1 6.9 + - + +
1336D ALA* 2.9 29.9 + - - +
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Residues in contact with THR1333 (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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115D TRP* 3.7 43.7 + - + +
116D PHE* 3.5 30.7 - - + -
123D ARG* 5.3 7.6 + - - +
1329D THR* 3.0 13.6 + - + +
1330D ARG* 2.3 35.4 + - - -
1332D LEU* 1.3 73.7 - - - +
1334D GLU* 1.3 61.4 + - - -
1336D ALA* 3.0 13.1 + - - +
1337D VAL* 3.0 19.7 + - - +
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Residues in contact with GLU1334 (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 ARG* 4.6 24.8 - - - +
1330D ARG 2.9 12.4 + - - +
1331D VAL* 3.7 10.6 - - - +
1333D THR* 1.3 81.4 + - - +
1335D ALA* 1.3 52.7 + - - +
1337D VAL* 3.0 18.0 - - + +
1340D LYS* 2.2 51.1 + - - +
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Residues in contact with ALA1335 (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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22D ILE* 3.3 25.5 - - + +
1319D PHE* 4.3 20.0 - - + -
1331D VAL* 2.8 18.4 + - + +
1332D LEU* 3.3 7.4 - - - +
1334D GLU* 1.3 81.2 + - - +
1336D ALA* 1.3 61.7 + - - +
1340D LYS* 3.2 41.7 + - + +
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Residues in contact with ALA1336 (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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1335C ILE* 4.9 12.3 - - + -
22D ILE* 3.4 28.0 - - + -
23D ALA* 4.3 4.3 - - - +
24D LEU* 2.9 24.3 - - + +
116D PHE* 4.9 8.7 - - + -
1332D LEU 2.9 15.3 + - - +
1333D THR* 3.0 6.4 + - - +
1335D ALA* 1.3 77.5 - - - +
1337D VAL* 1.3 58.4 + - - +
1339D GLY* 2.7 21.8 + - - -
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Residues in contact with VAL1337 (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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24D LEU* 4.0 8.5 - - + -
116D PHE* 3.6 24.9 - - + -
123D ARG* 5.3 12.3 - - + +
223D LEU* 6.4 2.2 - - + -
226D ALA* 5.5 3.3 - - - +
227D PHE* 5.0 14.7 - - + -
230D SER* 4.4 2.6 + - - -
232D ASN* 2.9 24.8 + - - +
237D MET* 5.4 7.6 - - + -
1333D THR 3.0 17.2 + - - +
1334D GLU* 3.0 31.2 - - + +
1336D ALA* 1.3 75.6 - - - +
1338D ALA* 1.3 59.1 + - + +
1340D LYS* 3.9 2.2 - - - +
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Residues in contact with ALA1338 (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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226D ALA* 5.3 12.1 - - + -
230D SER* 4.1 16.6 - - - -
232D ASN* 3.5 5.7 + - - +
1336D ALA 3.1 0.4 - - - -
1337D VAL* 1.3 81.1 - - + +
1339D GLY* 1.3 65.0 + - - +
1340D LYS* 3.1 35.9 + - + +
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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