Contacts of the strand formed by residues 1042 - 1048 (chain A) in PDB entry 3M5M
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 THR1042 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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995A VAL* 4.6 3.8 - - + -
1035A ILE* 3.5 29.4 - - + -
1036A VAL 3.3 8.3 - - - +
1037A SER* 3.3 19.3 + - - -
1041A GLN* 1.3 72.7 - - - +
1043A PHE* 1.3 64.1 + - - +
1109A ARG* 3.8 19.4 + - - +
1136A LYS* 5.9 0.2 - - - +
1137A GLY* 3.3 19.6 - - - -
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Residues in contact with PHE1043 (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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992A VAL* 4.9 2.7 - - + -
1035A ILE* 3.4 7.5 - - - +
1036A VAL* 2.8 57.8 + - + -
1038A THR* 4.1 16.2 - - + -
1041A GLN* 3.8 26.7 - - + +
1042A THR* 1.3 79.4 - - - +
1044A LEU* 1.3 62.1 + - - +
1054A THR* 3.3 32.3 - - + -
1055A VAL* 4.4 3.6 - - + -
1058A GLY* 3.3 38.4 - - - -
1059A ALA* 3.5 16.4 - - + -
1109A ARG* 4.5 0.7 - - - +
1137A GLY* 3.1 19.5 - - - +
1139A ALA* 3.6 12.1 - - + +
1183A SO4 4.3 4.9 - - - +
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Residues in contact with LEU1044 (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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998A ILE* 3.9 12.1 - - + -
1033A VAL* 4.4 10.3 - - + -
1034A GLN 3.2 14.1 - - - +
1035A ILE* 3.7 23.8 - - + -
1036A VAL* 4.2 2.5 - - - -
1043A PHE* 1.3 82.6 - - - +
1045A ALA* 1.3 57.3 + - - +
1054A THR* 2.7 28.4 + - - -
1107A VAL* 3.9 5.8 - - + +
1108A THR 3.9 8.3 - - - +
1109A ARG* 3.7 30.7 - - + +
1137A GLY 3.7 9.2 - - - +
1138A SER* 3.7 14.6 - - - +
1139A ALA 3.2 3.8 + - - +
1140A GLY* 3.3 8.8 - - - -
1141A GLY* 3.6 26.9 - - - +
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Residues in contact with ALA1045 (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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1032A GLU 3.8 0.7 - - - +
1033A VAL* 3.5 3.1 - - - +
1034A GLN* 2.8 34.1 + - + +
1036A VAL* 4.0 21.8 - - + -
1044A LEU* 1.3 76.0 - - - +
1046A THR* 1.3 61.5 + - - +
1052A LEU* 3.7 24.1 - - + +
1053A TRP 3.1 13.9 - - - +
1054A THR* 3.9 10.5 - - + -
1085A TRP* 4.9 2.0 - - + -
1140A GLY 3.7 1.1 - - - -
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Residues in contact with THR1046 (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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1032A GLU 3.4 7.2 - - - +
1033A VAL* 4.2 5.2 - - + +
1045A ALA* 1.3 75.4 + - - +
1047A SER* 1.3 66.6 + - - +
1048A ILE* 4.0 9.0 - - + -
1052A LEU* 3.7 3.4 - - - -
1053A TRP* 2.8 40.4 + - - +
1094A LEU* 3.6 30.7 - - + -
1140A GLY 2.8 22.7 + - - -
1141A GLY* 3.5 12.6 - - - -
1142A PRO* 3.5 15.5 - - + +
1153A ILE* 3.7 11.9 - - + -
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Residues in contact with SER1047 (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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1032A GLU* 2.9 13.7 + - - +
1046A THR* 1.3 72.7 - - - +
1048A ILE* 1.3 61.7 + - - +
1051A VAL 3.1 9.2 + - - -
1052A LEU* 3.7 11.7 - - - +
1087A ALA* 3.7 20.3 - - - +
1091A SER* 4.7 4.9 - - - -
1092A ARG 3.5 17.6 + - - +
1093A SER* 2.5 29.9 + - - -
1094A LEU* 2.9 27.4 + - - +
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Residues in contact with ILE1048 (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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1046A THR* 4.0 9.4 - - + -
1047A SER* 1.3 80.3 + - - +
1049A ASN* 1.3 83.2 + - - +
1050A GLY 3.2 1.4 + - - -
1051A VAL* 2.9 9.6 + - - +
1053A TRP* 3.1 27.5 + - + +
1093A SER* 4.0 0.7 - - - -
1094A LEU* 3.6 15.5 - - + +
1096A PRO* 4.1 6.5 - - + -
1142A PRO* 6.1 0.4 - - + -
1150A ALA* 3.7 27.6 - - + -
1152A GLY 5.2 3.6 - - - +
1153A ILE* 3.9 21.3 - - + -
1172A VAL* 4.0 21.8 - - + -
1175A LEU* 3.6 25.6 - - + -
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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