Contacts of the helix formed by residues 1228 - 1239 (chain D) in PDB entry 5UHA
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 GLU1228 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1211D THR* 5.5 1.0 - - - +
1215D LEU* 3.3 27.7 - - + +
1227D GLN* 1.3 90.3 + - + +
1229D THR* 1.3 65.2 + - - +
1230D THR* 3.3 4.5 - - - -
1231D ARG* 2.5 50.2 + - + +
1232D VAL* 2.9 22.7 + - + +
11G T 4.6 24.1 - - - +
12G G 3.7 13.3 + - - -
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Residues in contact with THR1229 (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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406D LEU* 4.1 21.6 + - + -
407D LYS* 4.1 13.2 - - - +
408D GLY 4.2 5.5 + - - -
413D PHE* 3.6 31.5 - - + +
1224D ALA* 3.2 29.5 + - + +
1226D PHE 5.5 0.2 + - - -
1227D GLN* 3.1 5.3 + - - -
1228D GLU* 1.3 74.3 + - - +
1230D THR* 1.3 63.5 + - - +
1232D VAL* 3.1 5.4 + - - +
1233D LEU* 3.1 34.2 + - + +
12G G 5.8 0.2 + - - -
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Residues in contact with THR1230 (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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105D TRP* 3.7 36.0 - - + +
386D ARG* 3.8 20.4 + - - +
403D SER* 4.2 5.6 - - - +
406D LEU* 6.1 1.8 - - + -
407D LYS* 3.5 43.8 + - + +
1228D GLU* 4.6 2.4 + - - -
1229D THR* 1.3 77.1 - - - +
1231D ARG* 1.3 63.7 + - - +
1233D LEU* 3.7 1.6 + - - +
1234D THR* 3.1 28.8 + - - +
11G T 4.5 4.3 + - - -
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Residues in contact with ARG1231 (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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110D VAL 5.1 9.2 - - - +
111D PRO* 6.3 0.4 - - - -
113D ARG* 4.2 19.2 - - - +
386D ARG* 5.7 0.2 - - - +
1215D LEU* 4.6 13.9 - - - +
1228D GLU* 2.5 56.2 + - + +
1230D THR* 1.3 82.6 + - - +
1232D VAL* 1.3 63.0 + - + +
1234D THR* 2.7 18.9 + - - -
1235D ASP* 3.5 18.0 + - - +
20H G 6.0 5.1 + - - -
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Residues in contact with VAL1232 (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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1215D LEU* 4.9 6.7 - - + -
1220D TRP* 4.0 16.2 - - + +
1223D ALA* 3.4 35.0 - - + +
1224D ALA* 3.8 23.1 - - + +
1227D GLN 3.5 7.6 - - - +
1228D GLU* 2.9 22.6 + - + +
1229D THR 3.1 5.8 + - - +
1231D ARG* 1.3 77.6 - - + +
1233D LEU* 1.3 66.2 + - + +
1235D ASP* 3.2 7.5 + - - +
1236D ALA* 3.0 20.6 + - + +
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Residues in contact with LEU1233 (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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1128C LEU* 3.7 27.1 - - + -
1133C LEU* 4.2 5.2 - - + -
12D ILE* 4.1 6.2 - - + +
105D TRP* 3.7 29.2 - - + -
406D LEU* 3.9 13.2 - - + -
413D PHE* 4.8 4.5 - - + -
1220D TRP* 3.6 36.6 - - + -
1224D ALA* 3.9 15.9 - - + -
1229D THR* 3.1 23.0 + - + +
1230D THR* 4.3 0.4 - - - +
1232D VAL* 1.3 74.1 - - + +
1234D THR* 1.3 67.1 + - - +
1236D ALA* 3.3 2.2 + - - +
1237D ALA* 2.8 28.5 + - - +
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Residues in contact with THR1234 (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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105D TRP* 3.4 59.4 - - + +
106D TYR* 3.7 16.6 - - + -
113D ARG* 4.2 17.8 + - - +
1230D THR* 3.1 11.4 + - - +
1231D ARG* 2.7 27.4 + - - -
1233D LEU* 1.3 76.0 - - - +
1235D ASP* 1.3 65.5 + - - +
1237D ALA* 3.2 10.7 + - - +
1238D ILE* 3.2 16.7 + - - +
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Residues in contact with ASP1235 (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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113D ARG* 3.3 35.7 + - - +
297D LYS* 3.7 24.6 + - - +
1231D ARG* 3.5 18.2 + - - +
1232D VAL* 3.2 9.0 + - - +
1233D LEU 3.2 0.6 - - - -
1234D THR* 1.3 79.9 + - - +
1236D ALA* 1.3 54.2 + - - +
1238D ILE* 2.6 29.5 + - - +
1239D ASN* 2.9 23.7 + - - +
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Residues in contact with ALA1236 (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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12D ILE* 3.4 16.5 - - + +
1220D TRP* 3.8 30.3 - - + -
1232D VAL* 3.0 14.4 + - + +
1233D LEU* 4.1 4.0 - - - +
1235D ASP* 1.3 79.2 - - - +
1237D ALA* 1.3 58.9 + - - +
1239D ASN* 3.9 1.6 - - - -
1240D CYS 3.3 2.6 + - - -
1241D ARG* 3.2 46.9 + - + +
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Residues in contact with ALA1237 (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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1133C LEU* 3.7 22.2 - - + -
12D ILE* 3.9 12.1 - - + +
13D GLY* 3.4 12.3 - - - +
14D LEU* 3.1 27.4 + - - +
106D TYR* 3.5 15.9 - - - +
307D ASN* 4.3 2.3 - - - +
1233D LEU 2.8 18.2 + - - +
1234D THR 3.5 4.7 - - - +
1235D ASP 3.0 0.2 + - - -
1236D ALA* 1.3 76.4 - - - +
1238D ILE* 1.3 61.7 + - - +
1240D CYS 4.1 2.0 + - - -
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Residues in contact with ILE1238 (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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14D LEU* 4.5 1.8 - - + -
106D TYR* 3.6 31.9 - - + -
113D ARG* 4.0 22.7 - - + -
298D VAL* 4.9 5.8 - - + +
301D ALA* 3.9 31.6 - - + +
302D PHE* 3.7 38.8 - - + -
307D ASN* 3.9 14.9 + - - +
312D MET* 4.8 1.8 - - - -
1234D THR 3.2 11.8 + - - +
1235D ASP* 2.6 18.4 + - - +
1237D ALA* 1.3 72.8 - - - +
1239D ASN* 1.3 60.1 + - - +
1240D CYS* 3.1 9.2 + - - -
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Residues in contact with ASN1239 (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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297D LYS* 4.9 19.1 + - - +
301D ALA* 4.0 17.2 - - - +
304D GLN* 3.5 24.0 + - - +
305D SER* 5.2 0.2 - - - -
1235D ASP* 2.9 26.7 + - - +
1236D ALA 3.8 0.2 + - - -
1238D ILE* 1.3 80.3 - - - +
1240D CYS* 1.3 69.7 + - - +
1241D ARG* 3.2 26.0 + - + +
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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