Contacts of the helix formed by residues 1125 - 1135 (chain A) in PDB entry 3L9X
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 SER1125 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1102A TRP* 3.4 29.9 - - - -
1121A PHE 4.0 0.2 + - - -
1122A ASP* 2.7 24.6 + - - +
1124A LEU* 1.3 78.0 - - - +
1126A GLN* 1.3 64.9 + - - +
1127A PRO* 3.5 0.9 - - - -
1128A LEU* 3.1 8.1 + - - +
1129A GLN* 2.9 35.0 + - - +
1139A TRP* 3.6 19.5 + - - -
1142A PRO* 4.7 5.6 - - - +
1118B HIS* 4.4 2.3 + - - -
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Residues in contact with GLN1126 (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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1122A ASP 4.3 0.2 + - - -
1123A VAL 3.0 18.3 + - - +
1125A SER* 1.3 78.7 + - - +
1127A PRO* 1.4 69.1 - - + +
1129A GLN* 3.3 4.4 + - - +
1130A ALA* 2.8 37.9 + - - +
1068B TYR* 5.9 0.4 - - - -
1113B PHE 5.0 0.8 + - - -
1115B ILE* 2.8 31.7 + - - +
1116B GLY* 3.9 2.5 - - - -
1117B ALA 3.7 7.1 + - - -
1118B HIS* 3.0 48.4 + - + +
1119B PRO* 4.3 1.4 - - - +
1120B GLY 5.8 0.6 + - - +
1123B VAL* 4.2 11.9 - - + +
1124B LEU* 3.8 18.9 - - + +
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Residues in contact with PRO1127 (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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1069A SER* 6.2 0.2 - - - +
1123A VAL 4.3 1.1 - - - +
1124A LEU* 3.4 17.0 - - - +
1126A GLN* 1.4 96.1 - - + +
1128A LEU* 1.3 59.6 + - + +
1130A ALA* 3.6 2.3 + - - +
1131A THR* 2.7 37.2 + - - -
1067B TRP 4.4 3.4 - - - +
1068B TYR* 3.6 38.7 - - + +
1069B SER* 4.4 10.8 - - - +
1124B LEU* 4.3 8.5 - - + +
1127B PRO* 4.7 18.8 - - + -
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Residues in contact with LEU1128 (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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1061A TRP* 3.8 27.2 - - + -
1070A ILE* 3.9 35.4 - - + -
1074A LEU* 5.9 0.2 - - + -
1078A ILE* 4.4 6.3 - - + -
1102A TRP* 3.4 51.4 - - + +
1124A LEU 5.0 3.8 - - - +
1125A SER 3.1 9.1 + - - +
1127A PRO* 1.3 83.9 - - + +
1129A GLN* 1.3 59.7 + - - +
1131A THR* 3.3 5.7 + - - +
1132A ALA* 2.9 29.5 + - - +
1139A TRP* 3.8 14.1 - - + -
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Residues in contact with GLN1129 (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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1125A SER* 2.9 28.5 + - - +
1126A GLN* 3.8 8.9 - - - +
1128A LEU* 1.3 75.9 - - - +
1130A ALA* 1.3 58.2 + - - +
1132A ALA* 3.3 0.7 + - - +
1133A ILE* 2.8 54.9 + - + +
1139A TRP* 3.6 44.6 + - + +
1116B GLY* 3.9 7.2 - - - -
1117B ALA* 3.3 41.2 + - - +
1118B HIS* 4.3 1.9 - - - -
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Residues in contact with ALA1130 (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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1126A GLN* 2.8 27.4 + - - +
1127A PRO 3.8 0.2 - - - +
1129A GLN* 1.3 78.6 - - - +
1131A THR* 1.3 61.2 + - - +
1134A TYR* 3.0 27.0 + - - +
1068B TYR* 3.7 33.2 - - + -
1115B ILE* 3.6 29.7 - - + +
1116B GLY 5.2 0.7 - - - +
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Residues in contact with THR1131 (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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1061A TRP* 4.1 10.1 - - + -
1078A ILE* 3.7 25.6 - - + +
1082A PHE* 3.9 13.9 - - + -
1127A PRO 2.7 23.0 + - - -
1128A LEU* 3.3 9.7 + - - +
1130A ALA* 1.3 75.9 - - - +
1132A ALA* 1.3 64.4 + - - +
1134A TYR* 3.4 1.2 + - - +
1135A CYS* 3.3 24.6 + - - -
1067B TRP* 3.5 36.9 + - + +
1068B TYR* 3.7 8.9 - - - -
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Residues in contact with ALA1132 (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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1061A TRP* 4.8 1.3 - - - -
1082A PHE* 5.2 0.4 - - - -
1100A LEU* 3.4 33.0 - - + -
1128A LEU 2.9 13.6 + - - +
1129A GLN 3.7 3.4 - - - +
1131A THR* 1.3 78.0 - - - +
1133A ILE* 1.3 62.2 + - - +
1135A CYS* 3.2 3.1 + - - +
1136A GLY 3.1 4.5 + - - -
1137A LEU* 2.9 45.4 + - + +
1139A TRP* 4.1 14.4 - - + -
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Residues in contact with ILE1133 (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 GLN* 2.8 52.6 + - + +
1130A ALA 4.2 2.5 - - - +
1132A ALA* 1.3 74.2 - - - +
1134A TYR* 1.3 64.0 + - - +
1136A GLY* 2.9 15.2 + - - -
1137A LEU 4.0 13.4 - - - +
1139A TRP* 4.7 11.9 - - + +
1115B ILE* 3.9 18.8 - - + -
1116B GLY* 4.0 14.1 - - - +
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Residues in contact with TYR1134 (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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1088A TYR* 3.9 37.4 - + + +
1096A HIS* 5.6 1.9 - - - -
1130A ALA 3.0 18.9 + - - +
1131A THR 3.7 4.9 - - - +
1132A ALA 3.3 0.2 - - - -
1133A ILE* 1.3 77.8 - - - +
1135A CYS* 1.3 58.1 + - - +
1136A GLY* 3.5 0.5 + - - -
1067B TRP* 3.7 25.1 - + + -
1068B TYR* 3.5 19.3 - - - +
1112B HIS* 3.8 29.3 - + - -
1115B ILE* 3.9 12.1 - - + +
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Residues in contact with CYS1135 (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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1082A PHE* 3.6 21.1 - - + -
1087A ALA* 3.4 32.2 - - - +
1088A TYR* 4.6 1.3 - - - -
1095A LEU* 3.7 27.7 - - + +
1096A HIS* 3.6 14.8 + - - -
1131A THR 3.3 13.7 + - - +
1132A ALA 3.2 4.5 + - - +
1133A ILE 3.1 0.8 - - - -
1134A TYR* 1.3 77.6 - - - +
1136A GLY* 1.3 58.0 + - - +
1137A LEU* 3.4 3.8 + - + -
1067B TRP* 3.5 33.2 - - - -
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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