Contacts of the strand formed by residues 1144 - 1153 (chain A) in PDB entry 3MP6
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 TRP1144 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1115A TRP* 4.3 2.5 - + - -
1132A ALA* 3.5 32.1 - - + -
1133A TYR 3.3 4.5 - - - -
1134A LYS* 3.5 40.5 - - + +
1135A PRO* 4.4 0.4 - - - -
1142A GLY* 3.4 13.6 + - - -
1143A GLU* 1.3 82.2 - - - +
1145A ILE* 1.3 61.4 + - - +
1181A LYS 3.9 18.6 - - - -
1182A GLU 3.5 21.8 - - - -
1183A LEU* 3.8 4.0 - - - -
1184A LEU* 3.9 14.6 - - + -
1202A LEU* 3.6 23.3 - - + +
1210A THR* 3.3 5.2 - - - +
1211A PHE* 2.7 42.5 + - + -
1250A PRO* 3.5 33.7 - - + +
1251A THR* 6.0 5.0 - - + +
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Residues in contact with ILE1145 (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* 3.4 3.2 - - - -
1133A TYR* 2.8 57.4 + - + +
1135A PRO* 4.1 18.6 - - + -
1143A GLU* 5.5 2.7 - - + +
1144A TRP* 1.3 78.4 - - - +
1146A GLN* 1.3 64.6 + - - +
1147A CYS* 3.4 8.5 + - - -
1163A ASP* 3.7 18.4 - - - +
1176A TYR* 3.9 32.1 - - + +
1209A THR 3.9 2.2 - - - -
1210A THR* 4.0 10.5 - - + +
1211A PHE* 4.5 0.9 - - - -
1P ALA* 3.6 25.4 - - + +
3P THR* 6.3 0.7 - - + -
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Residues in contact with GLN1146 (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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1130A GLU* 2.8 32.5 + - - +
1131A VAL 3.4 4.5 - - - -
1145A ILE* 1.3 72.9 - - - +
1147A CYS* 1.3 67.3 + - - +
1163A ASP* 3.9 8.8 - - - +
1164A PRO* 3.8 15.7 - - + +
1186A ILE* 3.8 20.3 - - + +
1204A ARG* 2.7 42.1 + - - +
1209A THR* 2.9 33.8 + - - +
1211A PHE* 3.9 10.1 - - + -
1245A LEU* 5.7 1.1 - - - +
1P ALA* 5.3 0.2 - - - +
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Residues in contact with CYS1147 (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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1130A GLU* 3.4 11.8 - - - +
1131A VAL* 2.8 41.0 + - + +
1133A TYR* 3.9 15.9 - - + -
1145A ILE* 3.8 18.4 - - - +
1146A GLN* 1.3 79.8 - - - +
1148A GLU* 1.3 59.9 + - - +
1161A VAL* 3.8 24.0 - - + -
1162A ARG 3.2 11.0 - - - +
1163A ASP* 3.7 24.5 - - - -
1164A PRO* 4.6 1.3 - - - -
1176A TYR* 4.6 2.0 - - - -
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Residues in contact with GLU1148 (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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1128A GLY* 5.4 4.8 - - - +
1129A SER 3.4 6.7 - - - +
1130A GLU* 3.3 17.7 + - - +
1147A CYS* 1.3 74.4 - - - +
1149A VAL* 1.3 63.9 + - - +
1150A LEU* 3.6 12.7 + - + +
1161A VAL* 3.2 4.0 - - - -
1162A ARG* 2.8 83.5 + - + +
1164A PRO* 4.4 16.4 - - + +
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Residues in contact with VAL1149 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1125A ILE* 3.8 12.6 - - + -
1126A LEU 3.3 22.0 - - - +
1127A VAL* 3.6 2.7 - - - +
1128A GLY* 2.9 26.3 + - - -
1129A SER* 2.9 20.8 + - - +
1131A VAL* 3.7 32.1 - - + -
1148A GLU* 1.3 74.6 - - - +
1150A LEU* 1.3 65.9 + - - +
1151A LYS 3.7 21.1 - - - +
1152A VAL* 3.8 14.6 - - + -
1159A PHE* 4.5 6.1 - - + -
1160A GLU 3.8 4.9 - - - +
1161A VAL* 4.1 7.2 - - + -
1183A LEU* 4.9 0.9 - - + -
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Residues in contact with LEU1150 (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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1127A VAL* 3.5 20.3 - - - +
1148A GLU* 3.8 30.7 - - + +
1149A VAL* 1.3 76.1 - - - +
1151A LYS* 1.3 63.7 + - + +
1160A GLU* 2.7 38.5 + - - +
1162A ARG* 3.7 44.6 - - + +
1175A VAL* 4.0 16.6 - - + -
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Residues in contact with LYS1151 (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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1127A VAL* 4.1 3.4 - - - -
1149A VAL* 3.7 3.7 - - - +
1150A LEU* 1.3 84.5 - - + +
1152A VAL* 1.3 67.6 + - - +
1153A VAL* 4.2 18.2 - - + -
1159A PHE* 3.3 5.1 - - - -
1160A GLU* 2.9 70.5 + - + +
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Residues in contact with VAL1152 (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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1109A GLU* 3.1 33.8 - - + +
1110A PHE 3.9 4.9 - - - -
1111A GLY 3.8 14.4 - - - +
1125A ILE 3.7 17.9 - - - +
1127A VAL* 4.0 18.3 - - + +
1149A VAL* 3.8 17.5 - - + -
1151A LYS* 1.3 78.7 - - - +
1153A VAL* 1.3 68.6 + - - +
1156A GLY* 3.7 25.6 - - - -
1158A ARG 3.7 2.7 - - - +
1159A PHE* 3.9 11.7 - - + -
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Residues in contact with VAL1153 (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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1109A GLU* 3.2 8.3 - - - -
1151A LYS* 4.4 21.8 - - + -
1152A VAL* 1.3 80.7 - - - +
1154A ALA* 1.3 72.5 + - + +
1156A GLY 3.2 8.7 + - - -
1157A THR 3.3 4.2 + - - -
1158A ARG* 2.9 47.1 + - + +
1159A PHE* 5.3 2.0 - - - -
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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