Contacts of the strand formed by residues 1130 - 1133 (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 GLU1130 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1128A GLY 4.7 5.1 - - - +
1129A SER* 1.3 73.2 - - - +
1131A VAL* 1.3 66.4 + - - +
1146A GLN* 2.6 37.3 + - - +
1147A CYS 3.4 5.9 - - - +
1148A GLU* 3.5 26.2 + - - +
1164A PRO* 5.4 6.0 - - - +
1185A LEU* 3.5 5.6 - - - +
1186A ILE* 3.2 41.2 + - + +
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Residues in contact with VAL1131 (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 ILE* 4.2 15.0 - - + -
1129A SER* 4.9 0.2 - - - -
1130A GLU* 1.3 81.6 - - - +
1132A ALA* 1.3 61.8 + - - +
1133A TYR* 4.9 1.6 - - + +
1146A GLN* 3.3 6.4 - - - +
1147A CYS* 2.9 46.3 + - + +
1149A VAL* 4.2 14.6 - - + -
1161A VAL* 4.4 4.5 - - + -
1183A LEU* 4.1 32.3 - - + -
1184A LEU 3.3 16.2 - - - +
1185A LEU* 3.9 15.5 - - + -
1186A ILE* 3.7 11.3 - - - +
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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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1131A VAL* 1.3 72.3 - - - +
1133A TYR* 1.3 60.2 + - - +
1144A TRP* 3.5 23.3 - - + -
1145A ILE 3.5 6.1 - - - -
1146A GLN* 4.6 0.7 - - - +
1183A LEU* 2.9 27.4 - - - +
1184A LEU* 2.9 17.4 + - + +
1186A ILE* 4.2 0.6 - - - +
1202A LEU* 5.4 0.4 - - + -
1211A PHE* 4.4 11.2 - - + -
1247A LEU* 3.6 29.6 - - + -
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Residues in contact with TYR1133 (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 VAL* 4.0 2.4 - - + -
1132A ALA* 1.3 73.6 - - - +
1134A LYS* 1.3 75.0 + - - +
1135A PRO* 3.1 19.5 - - + +
1136A ARG* 4.3 10.4 + - - +
1144A TRP* 3.1 4.1 - - - -
1145A ILE* 2.7 61.8 + - + +
1147A CYS* 3.7 20.2 - - + -
1161A VAL* 4.2 7.0 - - + -
1176A TYR* 3.3 51.6 - + + +
1177A LYS 4.3 6.4 + - - -
1178A CYS* 3.6 31.9 - - + -
1182A GLU* 3.2 23.6 + - - -
1183A LEU* 4.4 3.4 - - + -
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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