Contacts of the helix formed by residues 1127 - 1143 (chain B) in PDB entry 1AIS
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 ARG1127 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1126B PRO* 1.3 73.8 - - - +
1128B HIS* 1.3 59.2 + - - +
1130B GLU* 3.4 32.9 + - - +
1131B GLU* 2.9 35.9 + - + +
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Residues in contact with HIS1128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1126B PRO* 3.4 32.8 - - + +
1127B ARG* 1.3 78.8 + - - +
1129B VAL* 1.3 75.1 + - + +
1131B GLU* 3.9 6.4 - - - +
1132B GLU* 3.1 27.2 + - - +
1166B LEU* 3.7 23.8 - - + +
1168B VAL* 4.3 7.7 - - - +
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Residues in contact with VAL1129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1125B LEU* 4.4 15.7 - - + -
1126B PRO* 3.1 25.7 + - + +
1128B HIS* 1.3 82.2 - - + +
1130B GLU* 1.3 67.2 + - - +
1132B GLU* 3.1 4.0 + - - +
1133B ALA* 3.0 21.7 + - + +
1159B VAL* 4.7 0.7 - - - +
1162B ALA* 3.6 13.9 - - + +
1163B CYS* 3.8 29.2 - - - +
1166B LEU* 3.8 13.0 - - + -
1168B VAL* 3.6 32.3 - - + -
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Residues in contact with GLU1130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1113B LEU* 4.7 6.2 - - - +
1116B LEU* 3.3 29.6 - - + +
1117B ASP* 3.1 23.9 - - - +
1120B THR* 3.6 31.0 + - - +
1125B LEU* 4.9 4.3 - - - +
1126B PRO 3.1 9.1 + - - +
1127B ARG* 3.5 42.9 + - - +
1129B VAL* 1.3 81.0 - - - +
1131B GLU* 1.3 62.7 + - - +
1133B ALA* 3.2 6.6 + - - +
1134B ALA* 3.1 19.4 + - + +
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Residues in contact with GLU1131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1127B ARG* 2.9 27.2 + - + +
1128B HIS* 3.9 6.1 - - - +
1130B GLU* 1.3 76.0 - - - +
1132B GLU* 1.3 59.1 + - - +
1134B ALA* 3.6 7.7 + - - +
1135B ARG* 3.0 22.6 + - + +
1138B ARG* 3.6 23.7 + - - -
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Residues in contact with GLU1132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1128B HIS 3.1 19.0 + - - +
1129B VAL 3.1 5.6 + - - +
1131B GLU* 1.3 75.1 - - - +
1133B ALA* 1.3 60.0 + - - +
1135B ARG* 2.8 39.6 + - - +
1136B LEU* 2.9 32.5 + - + +
1162B ALA* 3.9 17.0 - - + -
1165B LEU* 3.9 21.1 - - + +
1166B LEU* 3.6 22.9 - - + +
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Residues in contact with ALA1133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1116B LEU* 4.0 10.3 - - + -
1129B VAL* 3.0 12.4 + - + +
1130B GLU* 3.2 12.3 + - - +
1132B GLU* 1.3 78.6 - - - +
1134B ALA* 1.3 61.0 - - - +
1136B LEU* 3.4 3.5 + - - +
1137B TYR* 3.0 23.2 + - - +
1155B MET* 4.4 2.5 - - - -
1158B CYS* 3.6 12.3 - - - +
1159B VAL* 3.8 37.2 - - + +
1162B ALA* 3.9 6.7 - - + +
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Residues in contact with ALA1134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1113B LEU* 3.7 16.2 - - + -
1116B LEU* 3.7 21.7 - - + +
1130B GLU* 3.1 8.1 + - + +
1131B GLU* 3.8 11.4 - - - +
1133B ALA* 1.3 80.7 - - - +
1135B ARG* 1.3 61.4 + - - +
1137B TYR* 3.1 8.8 + - - +
1138B ARG* 3.1 44.7 + - - +
1155B MET* 4.5 1.6 - - - -
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Residues in contact with ARG1135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1131B GLU* 3.0 22.7 + - - +
1132B GLU* 2.8 35.8 + - - +
1134B ALA* 1.3 76.5 - - - +
1136B LEU* 1.3 74.2 + - - +
1138B ARG* 3.2 26.6 + - - +
1139B GLU* 3.1 45.8 + - - +
1142B ARG* 5.4 5.9 + - - +
1165B LEU* 5.4 1.4 - - - +
1199B LEU* 6.0 0.6 - - - +
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Residues in contact with LEU1136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1132B GLU* 2.9 27.2 + - + +
1133B ALA 3.6 4.5 - - - +
1135B ARG* 1.3 88.4 - - - +
1137B TYR* 1.3 57.4 + - - +
1139B GLU* 3.1 17.0 + - - +
1140B ALA* 2.9 28.1 + - - +
1158B CYS* 3.8 34.5 - - - +
1161B ALA* 3.9 19.1 - - + -
1162B ALA* 4.1 7.6 - - - +
1165B LEU* 4.3 10.5 - - + -
1193B ILE* 4.6 2.9 - - + -
1197B LEU* 3.7 26.5 - - + +
1199B LEU* 4.1 17.5 - - + -
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Residues in contact with TYR1137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1108B ASN 4.8 1.4 + - - -
1109B LEU* 4.8 11.8 - - + +
1112B ALA* 3.8 22.9 - - + +
1133B ALA 3.0 13.2 + - - +
1134B ALA 3.1 9.6 + - - +
1136B LEU* 1.3 76.7 - - - +
1138B ARG* 1.3 62.0 + - + +
1140B ALA* 3.1 6.8 + - - +
1141B VAL* 2.9 43.5 + - + +
1145B LEU* 4.2 11.7 - - + +
1151B ILE* 3.2 40.9 - - - +
1154B VAL* 3.5 31.9 - - + -
1155B MET* 3.5 35.4 - - + -
1158B CYS* 3.7 6.9 - - - -
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Residues in contact with ARG1138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1109B LEU* 5.4 10.3 - - + -
1113B LEU* 5.2 3.6 - - - +
1131B GLU* 3.6 11.3 + - - -
1134B ALA* 3.1 38.7 + - - +
1135B ARG* 3.2 37.4 - - - +
1137B TYR* 1.3 75.1 - - + +
1139B GLU* 1.3 62.6 + - - +
1140B ALA 3.1 0.7 - - - -
1141B VAL* 3.3 19.0 + - + +
1142B ARG* 3.1 47.7 + - - +
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Residues in contact with GLU1139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1135B ARG* 3.1 49.2 + - - +
1136B LEU* 3.1 20.6 + - - +
1138B ARG* 1.3 77.5 - - - +
1140B ALA* 1.3 57.6 + - - +
1142B ARG* 4.0 20.6 + - - +
1143B LYS* 3.6 25.1 + - - +
1197B LEU* 3.4 36.1 - - + +
1198B ASN* 3.7 18.5 + - - +
1199B LEU* 4.7 2.1 - - - +
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Residues in contact with ALA1140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1136B LEU 2.9 11.9 + - - +
1137B TYR* 3.1 10.3 + - - +
1139B GLU* 1.3 78.6 - - - +
1141B VAL* 1.3 56.9 + - - +
1142B ARG 3.2 0.4 - - - -
1143B LYS* 2.8 35.9 + - - +
1145B LEU* 3.3 28.0 + - + -
1149B ARG* 5.8 2.2 - - - +
1193B ILE* 3.8 26.2 - - + -
1196B ASN* 5.6 3.1 - - - +
1197B LEU* 4.7 3.8 - - + -
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Residues in contact with VAL1141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1109B LEU* 4.5 30.1 - - + -
1137B TYR* 2.9 44.6 + - + +
1138B ARG* 3.3 15.9 + - + +
1140B ALA* 1.3 78.5 - - - +
1142B ARG* 1.3 64.2 + - + +
1143B LYS 3.1 0.9 + - - -
1144B GLY* 3.5 11.3 + - - -
1145B LEU* 4.6 10.5 - - + -
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Residues in contact with ARG1142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1135B ARG* 5.4 6.1 + - - +
1138B ARG* 3.1 39.7 + - - +
1139B GLU* 4.1 19.2 - - - +
1140B ALA 3.2 0.4 - - - -
1141B VAL* 1.3 78.5 - - + +
1143B LYS* 1.3 61.3 + - + +
1144B GLY 3.6 1.9 + - - -
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Residues in contact with LYS1143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1139B GLU* 3.6 11.9 - - - +
1140B ALA* 2.8 15.4 + - - +
1142B ARG* 1.3 82.3 - - + +
1144B GLY* 1.3 55.3 + - - +
1145B LEU 2.8 9.0 + - - -
1146B ILE 4.4 1.4 + - - -
1192B PHE* 6.0 0.3 - - - -
1196B ASN* 3.1 51.1 + - - +
1197B LEU* 3.6 32.7 - - + +
1198B ASN* 4.4 8.7 + - - +
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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