Contacts of the strand formed by residues 1210 - 1219 (chain A) in PDB entry 3MP1
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 THR1210 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1143A GLU* 3.7 20.5 + - + +
1144A TRP 3.5 13.0 - - - +
1145A ILE* 4.6 3.4 - - + +
1204A ARG* 3.2 3.8 - - - -
1205A TYR 3.2 24.8 + - - -
1208A THR* 3.2 4.3 + - - -
1209A THR* 1.3 82.6 - - - +
1211A PHE* 1.3 74.5 + - - +
1212A TYR* 3.5 33.0 + - + -
1P ALA* 4.2 8.3 - - - +
2P ARG 2.9 20.1 + - - -
3P THR* 3.8 9.9 - - - +
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Residues in contact with PHE1211 (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 ALA* 4.4 10.3 - - + -
1142A GLY 3.9 2.8 - - - +
1143A GLU* 3.8 3.8 - - - -
1144A TRP* 2.8 46.0 + - + +
1146A GLN* 3.8 34.3 - - + -
1186A ILE* 3.4 25.4 - - + -
1202A LEU* 3.4 30.5 - - + +
1203A ALA 3.2 4.9 - - - +
1204A ARG* 3.6 24.7 - - + -
1209A THR 4.2 1.8 - - - -
1210A THR* 1.3 80.2 - - - +
1212A TYR* 1.3 61.5 + - - +
1245A LEU* 3.7 21.8 - - + -
1247A LEU* 3.4 23.8 - - + -
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Residues in contact with TYR1212 (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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1142A GLY 6.2 0.2 - - - -
1143A GLU* 3.6 35.2 + - + -
1202A LEU* 3.6 4.8 - - - -
1203A ALA 2.9 27.2 + - - +
1205A TYR* 3.6 32.3 - + + -
1208A THR* 4.3 2.5 - - - -
1210A THR* 3.5 23.6 - - + +
1211A PHE* 1.3 74.1 - - - +
1213A PRO* 1.3 78.2 - - + +
1214A ALA 3.5 0.2 + - - -
1229A PHE* 3.7 17.7 - - + -
3P THR* 3.5 13.0 - - - -
4P M3L 2.9 68.6 + - + +
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Residues in contact with PRO1213 (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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1142A GLY* 3.7 35.2 - - - +
1201A VAL 3.7 6.7 - - - +
1202A LEU* 4.2 8.7 - - + -
1212A TYR* 1.3 95.4 - - + +
1214A ALA* 1.3 60.0 + - - +
1229A PHE* 3.4 4.9 - - - -
1230A ASP* 3.4 39.8 + - + +
1249A SER* 5.8 2.7 - - - +
1251A THR* 6.1 4.5 - - + -
4P M3L 6.0 0.7 - - - -
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Residues in contact with ALA1214 (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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1200A LYS* 3.6 5.9 - - - +
1201A VAL* 2.9 45.2 + - + +
1203A ALA* 4.6 1.1 - - + -
1212A TYR 4.1 0.9 - - - +
1213A PRO* 1.3 76.0 - - - +
1215A ILE* 1.3 67.5 + - - +
1227A LEU* 4.4 13.2 - - + -
1228A ARG 3.6 9.9 - - - +
1229A PHE* 3.6 26.7 - - + +
1230A ASP* 4.0 4.4 + - - -
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Residues in contact with ILE1215 (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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1198A GLY* 4.3 16.2 - - - +
1199A THR 3.7 7.9 - - - +
1200A LYS* 5.1 10.5 - - + -
1214A ALA* 1.3 80.3 - - - +
1216A VAL* 1.3 73.4 + - - +
1217A ILE* 3.6 1.1 + - + -
1227A LEU* 3.5 4.8 - - - -
1228A ARG* 2.9 45.3 + - + +
1230A ASP* 4.1 21.3 - - - +
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Residues in contact with VAL1216 (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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1195A TYR* 4.1 25.6 - - + +
1196A PRO 4.3 9.0 - - - +
1197A PRO* 4.4 0.8 - - + +
1198A GLY* 3.0 26.0 + - - -
1199A THR* 3.0 26.9 + - - +
1201A VAL* 3.7 30.1 - - + -
1215A ILE* 1.3 75.4 - - - +
1217A ILE* 1.3 62.6 + - - +
1218A GLY* 4.0 17.0 - - - +
1219A THR* 4.9 2.7 - - - +
1225A CYS* 4.9 5.2 - - + -
1226A ARG 4.0 0.4 - - - +
1227A LEU* 3.8 18.6 - - + -
1246A VAL* 4.8 1.8 - - + -
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Residues in contact with ILE1217 (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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1197A PRO* 3.2 23.1 - - - +
1215A ILE* 4.4 1.3 - - + +
1216A VAL* 1.3 75.5 - - - +
1218A GLY* 1.3 60.0 + - - +
1226A ARG* 2.9 37.1 + - + +
1227A LEU* 4.1 2.9 - - - -
1228A ARG* 4.1 35.4 - - + +
1238A GLU* 3.4 32.5 - - + +
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Residues in contact with GLY1218 (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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1197A PRO* 4.4 10.3 - - - -
1216A VAL* 3.7 5.7 - - - +
1217A ILE* 1.3 83.7 - - - +
1219A THR* 1.3 59.1 + - - -
1225A CYS* 3.7 0.9 - - - -
1226A ARG* 2.7 52.9 + - - +
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Residues in contact with THR1219 (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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1194A ASN* 3.0 42.1 - - - +
1195A TYR 3.8 14.6 + - - -
1197A PRO* 5.6 0.4 - - - +
1216A VAL* 4.9 1.7 - - - +
1218A GLY* 1.3 71.8 - - - -
1220A LYS* 1.3 66.8 + - - +
1221A ARG* 3.7 1.4 + - - -
1223A GLY* 2.8 30.3 - - - +
1224A THR 3.6 3.6 - - - +
1225A CYS* 4.5 10.6 - - - +
1226A ARG* 5.2 1.8 - - - -
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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