Contacts of the helix formed by residues 1172 - 1179 (chain B) 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 VAL1172 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1048B ILE* 4.3 16.4 - - + -
1049B ASN* 5.4 0.6 + - - +
1096B PRO* 4.5 18.8 - - + -
1097B CYS* 4.9 5.4 - - + +
1150B ALA* 3.2 40.2 - - + +
1151B VAL* 3.0 25.1 + - - +
1152B GLY* 3.8 5.2 - - - +
1170B ILE 3.7 0.2 + - - -
1171B PRO* 1.3 71.4 - - - +
1173B GLU* 1.3 82.9 + - - +
1175B LEU* 3.2 14.0 + - + +
1176B GLU* 3.0 29.3 + - - +
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Residues in contact with GLU1173 (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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1097B CYS 4.8 6.8 - - - +
1118B ARG* 4.6 11.0 + - - -
1121B ASP* 4.9 5.4 - - - +
1151B VAL 4.5 1.4 - - - +
1171B PRO* 3.5 18.0 - - + +
1172B VAL* 1.3 97.2 - - - +
1174B SER* 1.3 56.9 + - - +
1176B GLU* 3.3 17.3 + - - +
1177B THR* 3.0 30.9 + - - -
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Residues in contact with SER1174 (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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1080B LYS* 2.9 45.5 + - - +
1082B LEU* 5.2 0.4 - - - -
1170B ILE* 4.0 12.5 - - - +
1171B PRO* 2.9 25.0 + - - +
1173B GLU* 1.3 77.3 - - - +
1175B LEU* 1.3 65.4 + - - +
1177B THR* 3.3 4.7 + - - -
1178B THR* 3.0 20.2 + - - -
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Residues in contact with LEU1175 (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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1048B ILE* 3.7 32.3 - - + -
1049B ASN* 5.3 3.8 - - - +
1053B TRP* 3.8 39.3 - - + +
1082B LEU* 3.8 16.6 - - + -
1153B ILE* 4.0 10.1 - - + -
1170B ILE* 3.3 33.0 - - + +
1171B PRO 3.7 4.0 - - - +
1172B VAL* 3.2 18.8 + - + +
1174B SER* 1.3 74.5 - - - +
1176B GLU* 1.3 59.0 + - + +
1178B THR* 3.2 8.3 + - - -
1179B MET* 3.0 34.3 + - - +
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Residues in contact with GLU1176 (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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1049B ASN* 3.8 20.4 + - - +
1096B PRO* 3.9 25.8 - - - +
1172B VAL* 3.0 15.9 + - - +
1173B GLU* 3.5 24.0 + - - +
1174B SER 3.2 0.2 - - - -
1175B LEU* 1.3 77.9 - - - +
1177B THR* 1.3 61.8 + - - +
1179B MET* 3.3 24.6 + - - +
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Residues in contact with THR1177 (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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1080B LYS* 4.4 8.3 - - - +
1173B GLU* 3.0 15.6 + - - +
1174B SER* 3.7 9.0 - - - -
1175B LEU 3.3 0.2 - - - -
1176B GLU* 1.3 73.8 - - - +
1178B THR* 1.3 66.8 + - - +
1179B MET 3.5 4.5 + - - -
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Residues in contact with THR1178 (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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1053B TRP* 4.4 7.6 - - + -
1075B TYR* 3.7 39.9 - - + -
1077B ASN* 4.7 10.4 + - + +
1080B LYS* 2.8 35.2 + - - +
1082B LEU* 4.1 7.8 - - + +
1174B SER 3.0 8.1 + - - -
1175B LEU* 3.2 12.1 + - - +
1177B THR* 1.3 79.4 - - - +
1179B MET* 1.3 61.2 + - - +
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Residues in contact with MET1179 (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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1049B ASN* 3.8 46.2 - - + +
1051B VAL* 4.0 11.4 - - + -
1053B TRP* 3.8 27.8 - - + -
1075B TYR* 3.6 29.4 + - + +
1175B LEU 3.0 17.7 + - - +
1176B GLU* 3.6 18.8 - - - +
1177B THR 3.3 4.4 - - - -
1178B THR* 1.3 81.3 - - - +
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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