Contacts of the helix formed by residues 1220 - 1231 (chain D) in PDB entry 5D4D
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 ALA1220 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1041C GLU 3.6 24.9 + - - +
1042C ALA* 4.6 2.5 + - - -
1044C GLY* 5.6 1.4 - - - -
1103D HIS 5.4 0.2 - - - +
1105D ILE 4.0 7.6 - - - +
1106D VAL* 4.1 5.2 - - + -
1218D GLY 3.6 2.4 + - - -
1219D GLU* 1.3 71.6 - - - +
1221D VAL* 1.3 62.9 + - - +
1222D GLY 3.3 2.2 - - - -
1223D ILE* 4.3 7.4 - - + +
1224D VAL* 3.1 27.5 + - - +
1462D LEU* 4.1 16.8 - - + -
1474D ALA* 4.1 16.6 - - + +
1475D GLY 5.2 0.2 - - - +
17E TYR* 4.9 0.6 + - - -
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Residues in contact with VAL1221 (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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1105D ILE* 3.3 29.9 + - + +
1106D VAL* 4.3 4.0 - - - -
1107D VAL* 3.6 23.8 - - + -
1200D VAL* 4.1 14.4 - - + -
1205D TYR* 3.4 36.1 + - + +
1215D VAL* 4.6 0.4 - - + -
1219D GLU* 3.2 17.2 + - + +
1220D ALA* 1.3 72.4 - - - +
1222D GLY* 1.3 62.8 + - - +
1224D VAL* 3.8 8.1 - - - +
1225D ALA* 2.9 28.1 + - - +
1370D ILE* 3.7 11.6 - - + +
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Residues in contact with GLY1222 (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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1102D THR* 3.0 41.4 + - - -
1105D ILE* 3.0 16.7 + - - -
1221D VAL* 1.3 76.6 - - - +
1223D ILE* 1.3 65.9 + - - +
1225D ALA* 3.1 6.2 + - - +
1226D ALA 2.9 19.2 + - - -
1370D ILE* 4.5 3.1 - - - -
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Residues in contact with ILE1223 (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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1038C TRP* 3.4 31.6 - - + +
1041C GLU* 3.7 17.0 - - + +
1042C ALA* 3.9 7.6 - - + -
1099D VAL* 3.8 20.9 - - + +
1102D THR* 4.5 0.9 - - - -
1103D HIS* 3.7 31.0 - - + +
1105D ILE 4.9 0.2 + - - -
1220D ALA* 3.9 8.6 + - + +
1222D GLY* 1.3 74.2 - - - +
1224D VAL* 1.3 58.7 + - - +
1226D ALA* 3.3 3.3 + - - +
1227D GLN* 2.9 45.0 + - + +
1462D LEU* 3.8 22.7 - - + -
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Residues in contact with VAL1224 (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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1042C ALA* 3.9 27.6 - - + +
710D ARG* 4.1 13.5 - - + +
772D PRO* 3.8 28.5 - - + +
1205D TYR* 4.5 6.7 - - - +
1219D GLU* 4.2 9.6 - - - +
1220D ALA 3.1 19.5 + - - +
1221D VAL* 3.8 7.9 - - - +
1222D GLY 3.2 0.8 - - - -
1223D ILE* 1.3 76.4 - - - +
1225D ALA* 1.3 56.1 + - - +
1227D GLN* 3.6 7.5 + - - +
1228D SER* 2.7 41.1 + - - +
1367D HIS* 4.1 12.1 - - + -
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Residues in contact with ALA1225 (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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1102D THR* 5.2 0.2 - - + -
1221D VAL 2.9 19.2 + - - +
1222D GLY* 3.1 6.0 + - - +
1224D VAL* 1.3 74.3 - - - +
1226D ALA* 1.3 66.6 + - - +
1228D SER* 2.9 12.1 + - - -
1229D ILE* 2.9 21.6 + - + +
1367D HIS* 3.6 41.7 - - - +
1370D ILE* 4.2 13.2 - - + -
1371D VAL* 4.8 3.6 - - + -
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Residues in contact with ALA1226 (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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1095D THR* 4.1 6.6 - - - +
1098D LEU* 3.6 19.9 - - + +
1099D VAL* 3.5 44.6 - - + +
1102D THR* 3.8 1.8 + - - +
1222D GLY 2.9 14.5 + - - +
1223D ILE 3.8 2.2 - - - +
1225D ALA* 1.3 75.9 - - - +
1227D GLN* 1.3 58.8 + - - +
1229D ILE* 3.9 5.6 - - - +
1230D GLY* 2.9 26.5 + - - -
1371D VAL* 5.2 1.5 - - - +
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Residues in contact with GLN1227 (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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1035C MET 4.5 2.4 + - - -
1038C TRP* 3.5 41.2 + - + +
1039C ALA* 3.6 8.3 - - - +
1042C ALA* 3.2 21.3 - - - +
707D THR 5.3 1.4 + - - -
708D LEU 3.6 18.6 + - - +
709D HIS* 3.8 13.0 - - + +
710D ARG* 3.4 18.1 + - - +
1095D THR* 4.9 3.8 - - + -
1099D VAL* 5.1 7.6 - - + -
1223D ILE* 2.9 25.9 + - + +
1224D VAL* 4.0 5.6 - - - +
1226D ALA* 1.3 75.2 - - - +
1228D SER* 1.3 59.7 + - - +
1230D GLY* 4.4 0.9 - - - +
1231D GLU* 2.9 35.2 + - - +
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Residues in contact with SER1228 (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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709D HIS* 5.6 3.7 - - - +
772D PRO* 4.6 1.4 - - - +
773D ALA* 3.4 37.9 + - - +
1224D VAL* 2.7 27.6 + - - +
1225D ALA 2.9 4.7 + - - -
1227D GLN* 1.3 78.1 - - - +
1229D ILE* 1.3 57.8 + - - +
1231D GLU* 4.8 2.4 - - - +
1232D PRO* 3.3 19.2 - - - +
1363D LEU* 3.6 12.4 - - - +
1367D HIS* 3.8 23.0 - - - -
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Residues in contact with ILE1229 (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* 5.3 1.7 - - + +
1098D LEU* 3.8 14.4 - - + -
1225D ALA 2.9 17.2 + - - +
1228D SER* 1.3 77.7 - - - +
1230D GLY* 1.3 63.2 + - - +
1232D PRO* 3.3 10.9 - - - +
1233D GLY* 4.2 1.7 + - - -
1263D PHE* 3.6 32.8 - - + -
1356D TYR* 2.9 41.9 + - + +
1363D LEU* 4.1 13.0 - - + -
1367D HIS* 3.7 23.8 - - + +
1368D ILE* 4.2 5.4 - - + +
1371D VAL* 3.6 31.2 - - + -
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Residues in contact with GLY1230 (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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708D LEU* 5.7 3.1 - - - +
1091D SER* 3.6 9.5 + - - -
1094D LEU* 5.7 4.7 - - - -
1095D THR* 3.5 28.2 + - - -
1098D LEU* 4.6 3.1 - - - +
1226D ALA 2.9 17.1 + - - -
1227D GLN 4.0 0.2 - - - -
1229D ILE* 1.3 78.0 - - - +
1231D GLU* 1.3 65.3 + - - +
1233D GLY* 2.9 16.6 + - - -
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Residues in contact with GLU1231 (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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708D LEU* 3.7 52.1 + - + +
709D HIS* 3.7 31.8 + - + +
1227D GLN 2.9 19.7 + - - +
1228D SER* 4.8 2.2 - - - +
1230D GLY* 1.3 77.1 - - - +
1232D PRO* 1.3 80.5 - - + +
1233D GLY 3.1 1.2 + - - -
1234D THR* 4.2 8.1 + - - -
1235D GLN* 4.4 12.6 + - - -
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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