Contacts of the helix formed by residues 1254 - 1264 (chain D) in PDB entry 5D4C
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 GLN1254 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1237D THR 4.7 16.6 - - - +
1252D ILE* 5.9 2.7 - - + -
1253D THR* 1.3 80.6 - - - +
1255D GLY* 1.3 67.8 - - - +
1257D PRO* 3.3 17.2 - - - +
1258D ARG* 3.8 4.5 + - - -
1355D VAL* 5.4 1.1 - - - -
1358D ALA* 5.7 5.0 - - - +
1359D GLN* 5.6 2.6 + - - -
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Residues in contact with GLY1255 (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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1236D LEU* 4.2 8.1 - - - -
1237D THR 4.5 13.7 - - - -
1254D GLN* 1.3 73.4 - - - +
1256D LEU* 1.3 68.0 + - - -
1257D PRO* 4.2 0.4 - - - -
1258D ARG* 3.0 5.5 + - - +
1259D VAL* 3.0 20.6 + - - +
1355D VAL* 3.6 30.6 - - - +
1359D GLN* 5.5 1.8 - - - -
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Residues in contact with LEU1256 (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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1087D ARG* 3.7 31.2 - - + +
1090D ASP* 4.2 6.1 - - + -
1091D SER* 3.6 37.0 - - - +
1094D LEU* 3.9 27.6 - - + -
1233D GLY* 3.9 13.7 - - - +
1236D LEU* 3.7 24.4 + - + +
1255D GLY* 1.3 70.7 - - - -
1257D PRO* 1.4 70.8 - - + +
1259D VAL* 3.1 10.9 + - + +
1260D ILE* 2.9 37.5 + - + +
1356D TYR* 5.5 0.7 - - - +
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Residues in contact with PRO1257 (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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1087D ARG* 6.1 0.9 - - - -
1236D LEU 5.7 0.4 - - - +
1237D THR 6.0 0.7 - - - +
1253D THR* 3.8 19.1 - - + -
1254D GLN 3.3 12.8 - - - +
1255D GLY* 4.2 0.2 - - - -
1256D LEU* 1.4 94.0 - - + +
1258D ARG* 1.3 56.1 + - - +
1260D ILE* 3.4 8.2 + - + +
1261D GLU* 2.9 27.4 + - - +
1266D ARG* 5.8 0.7 + - - -
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Residues in contact with ARG1258 (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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1253D THR* 3.6 36.0 - - - +
1254D GLN 3.8 3.3 + - - -
1255D GLY 3.0 9.0 + - - +
1257D PRO* 1.3 75.7 - - - +
1259D VAL* 1.3 66.9 - - - +
1261D GLU* 2.6 46.3 + - - +
1262D LEU* 2.9 56.3 + - + +
1268D PRO* 4.5 3.2 - - - +
1329D ALA* 3.6 20.6 - - - +
1330D ILE 5.3 1.4 + - - -
1347D TYR* 3.3 25.9 + - - -
1351D GLU* 3.3 21.7 + - - +
1355D VAL* 3.9 16.6 - - + -
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Residues in contact with VAL1259 (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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1094D LEU* 3.7 16.4 - - + -
1236D LEU* 4.0 5.6 - - + -
1255D GLY 3.0 8.4 + - - +
1256D LEU* 3.4 11.7 - - + +
1258D ARG* 1.3 77.1 - - - +
1260D ILE* 1.3 56.9 + - - +
1262D LEU* 3.2 10.2 + - - +
1263D PHE* 2.9 53.5 + - + -
1352D ILE* 4.7 6.2 - - + +
1355D VAL* 3.6 37.5 - - + -
1356D TYR* 3.9 24.2 - - + +
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Residues in contact with ILE1260 (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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1090D ASP* 3.9 32.5 - - + +
1094D LEU* 3.8 25.1 - - + -
1097D LYS* 4.3 15.3 - - - +
1256D LEU* 2.9 30.4 + - + +
1257D PRO* 3.8 7.0 - - + +
1259D VAL* 1.3 73.0 - - - +
1261D GLU* 1.3 65.5 + - - +
1263D PHE* 4.5 5.2 - - - +
1264D GLU* 3.2 38.1 + - + +
1266D ARG* 4.3 15.3 + - - +
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Residues in contact with GLU1261 (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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1253D THR* 4.0 16.9 + - - +
1257D PRO 2.9 14.4 + - - +
1258D ARG* 2.6 50.4 + - - +
1260D ILE* 1.3 78.8 - - - +
1262D LEU* 1.3 56.9 + - + +
1265D ALA* 3.4 1.4 + - - -
1266D ARG* 3.1 57.2 + - + +
1267D ARG 4.8 0.3 - - - +
1268D PRO* 3.4 31.1 - - + +
1269D LYS 4.4 2.6 + - - -
1329D ALA* 4.6 1.4 - - - +
1332D PRO* 5.7 0.2 - - - +
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Residues in contact with LEU1262 (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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1258D ARG* 2.9 58.1 + - + +
1259D VAL* 3.2 7.4 + - - +
1261D GLU* 1.3 73.4 - - + +
1263D PHE* 1.3 60.2 + - - +
1264D GLU 3.1 2.0 - - - -
1265D ALA* 2.9 21.1 + - - +
1330D ILE 5.9 0.2 - - - +
1332D PRO* 5.4 6.1 - - + -
1347D TYR* 4.4 6.5 - - + -
1348D LEU* 4.0 25.8 - - + +
1351D GLU* 3.5 17.7 - - + +
1352D ILE* 3.4 47.6 - - + +
1355D VAL* 5.5 0.2 - - + -
1375D MET* 3.7 9.1 - - - +
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Residues in contact with PHE1263 (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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1094D LEU* 4.0 24.9 - - + -
1098D LEU* 4.0 10.3 - - + -
1229D ILE* 3.6 44.0 - - + -
1259D VAL* 2.9 40.3 + - + +
1260D ILE 4.4 2.0 - - - +
1262D LEU* 1.3 77.0 - - - +
1264D GLU* 1.3 56.9 - - + +
1265D ALA 3.3 0.2 - - - -
1352D ILE* 3.5 32.8 - - + -
1368D ILE* 4.5 4.5 - - + -
1371D VAL* 3.5 35.7 - - + -
1372D VAL* 5.4 0.4 - - + -
1375D MET* 3.3 18.9 - - - +
1424D VAL* 3.0 31.8 + - + +
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Residues in contact with GLU1264 (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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1094D LEU* 5.8 0.2 - - + -
1097D LYS* 2.9 25.0 + - + +
1260D ILE* 3.2 26.6 + - + +
1262D LEU 3.1 0.8 - - - -
1263D PHE* 1.3 77.1 - - + +
1265D ALA* 1.3 70.2 + - - +
1266D ARG* 3.1 36.7 + - + +
1423D GLY* 3.3 13.4 + - - -
1424D VAL* 3.8 10.5 + - + -
1425D THR* 2.5 42.3 + - - -
1426D LYS 4.9 0.5 + - - -
20H G 4.5 7.4 + - - +
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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