Contacts of the strand formed by residues 1200 - 1204 (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 LYS1200 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1198A GLY 3.6 5.8 + - - +
1199A THR* 1.3 79.7 - - - +
1201A VAL* 1.3 66.7 + - - +
1214A ALA 3.6 8.1 - - - +
1215A ILE* 4.8 11.0 - - + +
1248A PRO* 4.3 0.2 - - - +
1249A SER* 3.3 22.6 + - - +
1251A THR* 5.2 5.8 + - + +
1252A ALA* 3.5 38.5 - - + +
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Residues in contact with VAL1201 (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* 3.9 12.6 - - + -
1199A THR* 3.7 16.8 - - + -
1200A LYS* 1.3 81.4 - - - +
1202A LEU* 1.3 63.8 + - - +
1213A PRO* 3.7 3.8 - - - +
1214A ALA* 2.9 47.2 + - + +
1216A VAL* 3.7 19.3 - - + -
1227A LEU* 4.5 5.8 - - + -
1246A VAL* 3.5 30.1 - - + -
1247A LEU 2.8 21.1 - - - +
1249A SER* 3.9 6.9 + - - +
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Residues in contact with LEU1202 (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* 5.4 1.3 - - + -
1142A GLY 4.5 3.6 - - - +
1144A TRP* 3.9 37.0 - - + +
1184A LEU* 3.3 32.5 - - + -
1201A VAL* 1.3 76.8 - - - +
1203A ALA* 1.3 60.4 + - - +
1211A PHE* 3.4 21.4 - - + +
1212A TYR 3.6 13.7 - - - +
1213A PRO* 4.2 12.3 - - + -
1245A LEU 3.5 0.3 - - - +
1247A LEU* 2.8 35.2 + - + +
1248A PRO 4.0 5.6 - - - +
1249A SER* 4.3 8.3 - - - +
1250A PRO* 3.4 16.8 - - + -
1251A THR* 5.4 3.4 - - + -
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Residues in contact with ALA1203 (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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1201A VAL* 3.9 1.4 + - + -
1202A LEU* 1.3 76.3 - - - +
1204A ARG* 1.3 63.4 - - - +
1205A TYR 3.4 1.2 + - - -
1211A PHE* 3.7 2.9 - - - -
1212A TYR 2.9 29.6 + - - +
1214A ALA* 4.6 2.0 - - + -
1227A LEU* 3.3 33.2 - - + -
1229A PHE* 3.6 18.5 - - + -
1241A VAL* 4.4 4.7 - - + -
1245A LEU 3.1 9.9 - - - +
1246A VAL* 4.2 8.1 - - + +
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Residues in contact with ARG1204 (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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1146A GLN* 3.0 39.2 + - - +
1203A ALA* 1.3 71.9 - - - +
1205A TYR* 1.3 65.0 + - - +
1206A PRO 3.7 1.2 - - - -
1208A THR 3.7 24.9 + - - +
1209A THR* 4.1 9.8 - - - +
1210A THR 3.2 18.2 - - - +
1211A PHE* 3.6 24.0 - - + -
1229A PHE* 4.5 0.7 - - - -
1241A VAL* 3.8 20.8 - - - +
1245A LEU* 3.1 47.7 + - + +
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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