Contacts of the helix formed by residues 1220 - 1234 (chain I) in PDB entry 3AOI
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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1041H GLU 4.0 20.4 - - - +
1042H ALA* 4.1 5.9 + - - +
1105I ILE 4.2 0.2 - - - -
1106I VAL* 3.9 13.1 - - - +
1218I GLY 4.0 2.2 + - - -
1219I GLU* 1.3 70.2 - - - +
1221I VAL* 1.3 65.7 + - - +
1222I GLY 3.3 2.2 - - - -
1223I ILE* 3.2 23.1 + - + +
1224I VAL* 3.2 23.0 + - - +
1462I LEU* 4.6 3.8 - - + -
1474I ALA* 4.2 15.1 - - + +
1475I GLY* 4.7 1.9 - - - +
17J TYR* 4.2 1.8 + - - -
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Residues in contact with VAL1221 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1105I ILE* 4.0 8.9 + - + -
1106I VAL* 4.3 0.4 - - - +
1107I VAL* 3.6 26.0 - - + -
1200I VAL* 6.0 2.7 - - + -
1205I TYR* 3.2 52.5 - - + +
1215I VAL* 5.0 1.1 - - + -
1219I GLU* 2.6 24.9 + - + +
1220I ALA* 1.3 69.2 - - - +
1222I GLY* 1.3 71.6 + - - +
1223I ILE 3.0 0.3 + - - -
1224I VAL* 3.2 7.9 + - + -
1225I ALA* 2.9 20.1 + - - +
1370I ILE* 3.2 23.8 - - + -
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Residues in contact with GLY1222 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1102I THR* 2.5 43.6 + - - -
1105I ILE* 2.9 31.1 + - - +
1221I VAL* 1.3 81.7 - - - +
1223I ILE* 1.3 61.0 + - - +
1225I ALA* 3.3 2.3 + - - +
1226I ALA 3.1 8.3 + - - -
1370I ILE* 4.6 3.4 - - - -
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Residues in contact with ILE1223 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1038H TRP* 3.8 14.6 - - + +
1041H GLU* 3.6 17.3 - - + +
1042H ALA* 3.4 17.3 - - + +
1099I VAL* 5.3 8.7 - - + -
1102I THR* 4.2 2.5 - - - +
1103I HIS* 4.2 19.1 - - + -
1105I ILE 5.4 0.2 - - - +
1220I ALA* 3.4 19.1 - - + +
1221I VAL 3.1 0.2 - - - -
1222I GLY* 1.3 73.3 - - - +
1224I VAL* 1.3 56.8 + - - +
1226I ALA* 2.6 31.6 + - + +
1227I GLN* 2.8 37.9 + - + +
1462I LEU* 3.4 34.3 - - + -
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Residues in contact with VAL1224 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1042H ALA* 3.7 27.6 - - + +
710I ARG* 4.4 17.5 - - + +
772I PRO* 4.3 18.5 - - + +
1205I TYR* 4.2 6.7 - - + +
1208I ASP 6.0 1.1 - - - +
1219I GLU* 5.0 10.8 - - + +
1220I ALA 3.4 18.4 - - - +
1221I VAL* 3.5 8.3 - - + +
1223I ILE* 1.3 79.4 - - - +
1225I ALA* 1.3 49.9 + - - +
1227I GLN* 3.7 9.4 - - - +
1228I SER* 2.5 36.4 + - - -
1367I HIS* 3.9 19.3 - - + -
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Residues in contact with ALA1225 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1102I THR* 5.6 0.2 - - - -
1221I VAL 2.9 10.9 + - - +
1222I GLY 3.6 4.0 - - - +
1223I ILE 2.7 4.0 + - - -
1224I VAL* 1.3 72.7 - - - +
1226I ALA* 1.3 61.4 + - - +
1228I SER* 2.9 11.6 + - - -
1229I ILE* 2.9 30.4 + - - +
1367I HIS* 3.4 21.5 - - + +
1370I ILE* 3.3 39.3 - - + -
1371I VAL* 5.0 3.1 - - + -
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Residues in contact with ALA1226 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1095I THR* 4.1 4.0 - - - +
1098I LEU* 3.1 21.6 - - + +
1099I VAL* 3.7 34.1 - - + +
1102I THR* 3.2 24.8 + - - +
1222I GLY 3.1 2.0 + - - -
1223I ILE* 2.6 15.2 + - - +
1225I ALA* 1.3 75.6 - - - +
1227I GLN* 1.3 61.5 + - - +
1229I ILE* 4.9 0.9 - - - -
1230I GLY* 3.0 18.7 + - - -
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Residues in contact with GLN1227 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1035H MET 5.3 2.0 + - - -
1038H TRP* 4.6 7.4 - - + +
1039H ALA* 4.0 14.8 - - - +
1042H ALA* 3.0 31.1 - - - +
707I THR 5.4 0.2 + - - -
708I LEU 3.6 12.5 + - - +
709I HIS* 3.1 18.9 - - + +
710I ARG* 3.1 29.5 + - - +
1095I THR* 4.1 13.7 - - + +
1099I VAL* 5.6 1.6 - - + -
1223I ILE* 2.8 23.2 + - + +
1224I VAL* 3.7 10.6 + - - +
1226I ALA* 1.3 73.6 - - + +
1228I SER* 1.3 58.0 + - - +
1229I ILE 2.9 3.8 - - - -
1230I GLY* 2.7 22.5 + - - -
1231I GLU* 3.1 16.7 + - - +
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Residues in contact with SER1228 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709I HIS* 5.5 2.4 - - - +
772I PRO* 4.4 2.0 - - - -
773I ALA* 3.7 37.7 - - - +
1224I VAL 2.5 23.0 + - - -
1225I ALA* 2.9 17.2 + - - -
1227I GLN* 1.3 74.9 - - - +
1229I ILE* 1.3 55.7 + - - +
1231I GLU* 5.0 3.3 - - - +
1232I PRO* 3.3 23.9 - - - +
1363I LEU* 4.2 12.1 - - - +
1367I HIS* 3.5 17.8 - - - -
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Residues in contact with ILE1229 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1094I LEU* 3.1 15.8 - - + +
1098I LEU* 3.2 21.3 - - + -
1225I ALA 2.9 22.4 + - - +
1227I GLN 2.9 1.0 - - - -
1228I SER* 1.3 79.3 - - - +
1230I GLY* 1.3 62.6 + - - +
1232I PRO* 3.7 5.9 - - - +
1233I GLY 4.0 0.2 + - - -
1263I PHE* 4.1 15.7 - - + -
1356I TYR* 3.3 22.9 + - + +
1363I LEU* 4.0 9.2 - - + -
1367I HIS* 3.5 13.9 - - + +
1368I ILE* 3.5 33.4 - - + -
1371I VAL* 3.5 30.3 - - + -
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Residues in contact with GLY1230 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1092I GLY* 5.1 4.0 - - - -
1094I LEU* 4.0 5.2 - - - +
1095I THR* 2.8 29.8 + - - -
1098I LEU* 3.8 8.3 - - - -
1226I ALA 3.0 9.5 + - - -
1227I GLN 2.7 6.7 + - - -
1229I ILE* 1.3 77.5 - - - +
1231I GLU* 1.3 66.9 + - - +
1233I GLY* 2.8 17.0 + - - -
1234I THR* 4.0 2.9 + - - -
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Residues in contact with GLU1231 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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708I LEU* 4.3 37.3 + - + +
709I HIS* 3.3 34.2 + - + +
773I ALA* 4.9 11.4 - - - +
1095I THR* 3.3 4.7 + - - +
1227I GLN 3.1 10.6 + - - +
1228I SER* 5.0 2.6 - - - +
1230I GLY* 1.3 69.2 - - - +
1232I PRO* 1.3 79.4 - - + +
1233I GLY 2.9 0.5 + - - -
1234I THR* 2.8 30.1 + - - -
1235I GLN* 3.7 5.2 - - - +
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Residues in contact with PRO1232 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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773I ALA* 6.0 2.2 - - + -
1228I SER 3.3 26.0 - - - +
1229I ILE 3.7 2.2 - - - +
1230I GLY 3.3 3.8 - - - -
1231I GLU* 1.3 105.8 - - + +
1233I GLY* 1.3 62.2 + - - +
1235I GLN* 2.9 25.2 + - - +
1236I LEU* 3.6 12.4 - - - +
1356I TYR* 3.4 27.1 - - + -
1361I VAL* 3.7 28.2 - - + +
1363I LEU* 5.8 0.2 - - + -
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Residues in contact with GLY1233 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1087I ARG* 5.1 1.7 - - - +
1094I LEU* 4.4 15.0 - - - -
1229I ILE 4.0 2.4 + - - -
1230I GLY 2.8 18.4 + - - -
1232I PRO* 1.3 75.7 - - - +
1234I THR* 1.3 61.7 - - - +
1235I GLN 3.0 0.7 - - - -
1236I LEU* 3.0 36.8 + - - +
1256I LEU* 4.8 11.5 - - - +
1356I TYR* 4.5 0.8 - - - -
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Residues in contact with THR1234 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
708I LEU* 4.6 16.3 - - + +
1087I ARG* 2.9 61.8 + - - +
1088I THR* 4.3 17.0 - - + +
1092I GLY* 4.9 12.6 + - - +
1230I GLY 4.0 2.7 + - - -
1231I GLU* 2.8 19.0 + - - -
1232I PRO 2.9 0.2 + - - -
1233I GLY* 1.3 74.0 - - - +
1235I GLN* 1.3 64.2 + - - +
1236I LEU 3.5 0.4 - - - -
43Y TYR* 4.8 4.0 - - + +
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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