Contacts of the helix formed by residues 1121 - 1136 (chain A) in PDB entry 3CMT
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 THR1121 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1119A PRO* 3.9 4.5 - - - +
1120A ASP* 1.3 86.9 - - + +
1122A GLY* 1.3 63.0 + - - +
1123A GLU* 3.7 13.8 + - - +
1124A GLN* 3.1 27.5 + - - +
1125A ALA* 3.1 20.4 + - - +
1150A THR 3.5 9.0 - - - -
1152A LYS* 3.9 36.5 - - + +
1155A ILE* 3.9 14.6 - - + -
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Residues in contact with GLY1122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1121A THR* 1.3 69.3 - - - +
1123A GLU* 1.3 65.3 + - - +
1125A ALA* 3.2 5.5 + - - +
1126A LEU* 3.1 27.3 + - - +
1149A LEU* 3.9 31.0 - - - -
1150A THR 2.7 21.9 + - - +
1170A MET* 4.1 8.5 - - - -
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Residues in contact with GLU1123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A ILE* 3.4 25.8 - - - +
160A GLY* 4.0 14.1 - - - -
1121A THR* 3.8 5.4 - - - +
1122A GLY* 1.3 76.1 - - - +
1124A GLN* 1.3 52.4 + - - +
1126A LEU* 3.3 6.4 + - - +
1127A GLU* 2.8 39.9 + - - +
1151A PRO* 3.5 7.3 - - - +
1152A LYS* 2.7 47.7 + - + +
1166A LEU* 4.8 5.2 - - - +
1170A MET* 3.6 27.9 - - + +
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Residues in contact with GLN1124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1118A GLN 4.9 0.5 - - - +
1119A PRO* 3.4 9.6 - - + +
1120A ASP* 3.4 48.2 + - - +
1121A THR* 3.1 20.3 + - - +
1123A GLU* 1.3 78.3 - - - +
1125A ALA* 1.3 62.9 + - - +
1127A GLU* 3.2 2.0 + - - +
1128A ILE* 2.9 39.8 + - + +
2021A PHE* 3.6 51.8 + - + +
2025A SER* 4.4 9.4 - - - +
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Residues in contact with ALA1125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1093A ILE* 4.0 12.5 - - + +
1119A PRO* 3.6 30.5 - - + +
1121A THR 3.1 6.6 + - - +
1122A GLY 3.2 9.6 + - - +
1124A GLN* 1.3 80.4 - - - +
1126A LEU* 1.3 59.2 + - + +
1128A ILE* 3.5 6.7 + - - +
1129A CYS* 3.2 29.0 + - - -
1143A VAL* 5.5 2.0 - - + -
1149A LEU* 3.8 23.1 - - + -
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Residues in contact with LEU1126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A ILE* 3.5 25.9 - - + +
1122A GLY 3.1 17.7 + - - +
1123A GLU* 3.9 2.7 - - - +
1125A ALA* 1.3 75.7 - - + +
1127A GLU* 1.3 60.5 + - - +
1128A ILE 3.2 0.2 - - - -
1129A CYS* 3.3 10.9 + - - +
1130A ASP* 3.0 22.9 + - - +
1143A VAL* 5.6 1.3 - - + -
1149A LEU* 4.2 7.6 - - + -
1170A MET* 3.9 22.7 - - + -
1171A MET* 3.5 35.7 - - + -
1174A ALA* 3.8 23.1 - - + -
1178A LEU* 4.4 5.9 - - + +
1191A PHE* 4.1 22.9 - - + -
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Residues in contact with GLU1127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A GLU* 3.7 30.7 - - + +
159A ILE* 3.0 50.4 + - + +
1123A GLU* 2.8 21.2 + - + +
1124A GLN 3.6 3.8 - - - +
1126A LEU* 1.3 75.1 - - - +
1128A ILE* 1.3 58.5 + - - +
1130A ASP* 3.4 6.6 + - - +
1131A ALA* 3.0 28.4 + - - +
1134A ARG* 5.1 8.3 + - - -
1177A LYS* 3.5 11.0 + - - -
2020A GLN* 4.5 7.1 - - - +
2021A PHE* 3.7 19.4 - - + -
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Residues in contact with ILE1128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1093A ILE* 3.9 22.2 - - + -
1117A SER* 3.5 22.7 - - - +
1119A PRO* 4.7 1.3 - - + -
1124A GLN* 2.9 40.9 + - + +
1125A ALA* 3.6 9.0 - - - +
1127A GLU* 1.3 74.3 - - - +
1129A CYS* 1.3 65.5 + - - +
1131A ALA* 3.3 6.8 + - - +
1132A LEU* 3.0 36.0 + - + +
2017A ILE* 3.9 27.8 - - + -
2021A PHE* 4.3 9.0 - - + -
2025A SER* 4.5 4.9 - - - +
2026A ILE* 4.3 13.0 - - + -
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Residues in contact with CYS1129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1093A ILE* 4.1 5.4 - - - -
1125A ALA 3.2 16.3 + - - -
1126A LEU* 3.3 17.0 + - - +
1128A ILE* 1.3 78.9 - - - +
1130A ASP* 1.3 52.0 + - - +
1132A LEU* 3.3 3.8 + - - +
1133A ALA* 2.7 36.0 + - - +
1141A ILE* 3.9 27.5 - - + +
1143A VAL* 3.6 30.7 - - - -
1178A LEU* 4.1 16.6 - - + -
1182A LEU* 5.6 0.2 - - - +
1189A LEU* 4.7 9.4 - - + -
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Residues in contact with ASP1130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A ILE 5.2 0.3 - - - +
159A ILE* 4.2 9.9 - - + -
1126A LEU 3.0 16.8 + - - +
1127A GLU* 3.7 7.9 - - - +
1128A ILE 3.3 0.2 - - - -
1129A CYS* 1.3 74.7 - - - +
1131A ALA* 1.3 57.4 + - - +
1133A ALA* 3.3 2.1 + - - +
1134A ARG* 2.5 60.5 + - - +
1177A LYS* 3.4 35.1 + - - +
1178A LEU* 3.6 20.7 - - + +
1181A ASN* 2.8 23.4 - - - +
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Residues in contact with ALA1131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1127A GLU 3.0 16.6 + - - +
1128A ILE 3.5 5.2 - - - +
1130A ASP* 1.3 77.1 - - - +
1132A LEU* 1.3 57.3 + - - +
1134A ARG* 3.4 22.7 + - - +
1135A SER* 3.0 28.8 + - - -
2013A ALA* 4.4 6.5 - - + +
2016A GLN* 5.3 9.2 - - + +
2017A ILE* 3.9 25.4 - - + -
2021A PHE* 6.5 0.7 - - + -
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Residues in contact with LEU1132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1091A ALA* 3.7 29.6 - - + -
1093A ILE* 4.7 4.7 - - + -
1115A LEU* 4.7 2.0 - - + -
1128A ILE* 3.0 34.0 + - + +
1129A CYS 3.7 2.7 - - - +
1131A ALA* 1.3 72.5 - - - +
1133A ALA* 1.3 67.4 + - - +
1135A SER* 2.7 24.2 + - - +
1136A GLY* 3.6 1.6 + - - -
1138A VAL* 3.8 28.9 + - + +
1141A ILE* 3.8 17.3 - - + -
1187A THR* 5.5 0.2 - - - -
2010A LEU* 5.5 0.4 - - + -
2013A ALA* 5.0 4.3 - - + -
2014A LEU* 4.6 13.9 - - + -
2017A ILE* 3.9 19.7 - - + -
2026A ILE* 4.2 13.9 - - + -
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Residues in contact with ALA1133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1129A CYS 2.7 22.3 + - - +
1130A ASP* 3.5 7.4 - - - +
1132A LEU* 1.3 75.3 - - - +
1134A ARG* 1.3 57.6 + - - +
1136A GLY* 3.1 2.6 + - - -
1141A ILE* 4.2 3.7 - - + +
1178A LEU* 4.8 2.5 - - + -
1181A ASN* 4.0 20.4 - - + +
1182A LEU* 4.0 26.0 - - + -
1185A SER* 2.5 31.8 + - - -
1187A THR* 4.1 9.4 + - - -
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Residues in contact with ARG1134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A ILE 5.6 2.4 + - - -
1127A GLU* 5.1 8.3 + - - -
1130A ASP* 2.5 55.6 + - - +
1131A ALA* 3.6 24.7 - - - +
1133A ALA* 1.3 72.1 - - - +
1135A SER* 1.3 62.8 + - - +
1136A GLY* 3.2 1.7 + - - -
1177A LYS* 5.0 1.2 - - - +
1181A ASN* 3.3 34.0 + - - +
1185A SER* 4.2 4.9 + - - -
2016A GLN* 5.1 10.7 - - - +
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Residues in contact with SER1135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1131A ALA 3.0 15.7 + - - -
1132A LEU* 2.7 22.0 + - - +
1134A ARG* 1.3 75.9 - - - +
1136A GLY* 1.3 59.0 + - - +
1137A ALA* 3.1 18.8 + - - +
1138A VAL* 4.1 3.5 + - - +
2009A ALA* 3.7 29.8 - - - +
2010A LEU* 5.1 0.6 - - - +
2013A ALA* 3.7 24.4 - - - +
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Residues in contact with GLY1136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1132A LEU 3.6 0.8 + - - -
1133A ALA 3.1 10.9 + - - -
1134A ARG 3.1 4.6 - - - -
1135A SER* 1.3 77.9 + - - +
1137A ALA* 1.3 59.3 + - - +
1138A VAL 3.6 6.1 - - - +
1139A ASP* 5.7 0.5 - - - +
1185A SER* 4.0 22.9 - - - +
2006A LYS* 4.0 15.7 - - - +
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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