Contacts of the strand formed by residues 1082 - 1086 (chain A) in PDB entry 3F2B
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 THR1082 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1000A TYR* 5.0 1.3 - - - -
1001A ARG* 3.2 22.4 - - + +
1002A ALA 4.0 4.3 - - - +
1003A GLY* 3.8 20.9 - - - -
1048A GLY 4.0 3.3 + - - +
1049A GLN* 4.4 1.6 - - + -
1069A ILE* 3.1 9.5 - - - +
1070A GLN* 2.8 41.7 + - - +
1071A TYR 3.5 2.8 - - - -
1072A PRO* 3.3 43.2 - - + +
1080A TRP* 3.9 1.5 + - + +
1081A ARG* 1.3 76.6 - - - +
1083A THR* 1.3 64.4 + - - +
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Residues in contact with THR1083 (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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1000A TYR* 4.1 16.6 - - + -
1001A ARG 3.2 10.8 + - - +
1002A ALA* 3.7 3.3 - - - +
1003A GLY* 2.9 30.0 + - - -
1055A ILE* 4.3 17.0 - - + -
1063A ILE* 4.5 7.9 - - + -
1067A THR* 4.1 22.2 - - + -
1068A PRO 3.7 4.5 - - - -
1069A ILE* 4.5 1.6 - - - +
1070A GLN* 4.6 3.0 - - - +
1082A THR* 1.3 78.7 + - - +
1084A HIS* 1.3 64.0 + - - +
1085A PHE 2.7 23.6 + - - +
1086A ASP* 4.6 1.9 - - - -
1087A PHE* 5.5 0.2 - - - -
1090A ILE* 4.6 7.3 - - + +
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Residues in contact with HIS1084 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A VAL* 3.4 23.1 - - + +
383A VAL* 3.3 43.5 + - + -
384A GLN* 2.6 59.0 + - + +
638A VAL* 3.8 17.7 - - + +
642A HIS* 4.4 2.5 - + - -
1005A ILE* 3.7 4.2 - - - +
1044A LYS* 5.3 0.2 - - - -
1067A THR* 3.3 1.1 + - - +
1068A PRO* 2.7 38.8 + - + +
1069A ILE* 4.2 1.8 - - - +
1070A GLN* 2.7 32.5 + - - +
1082A THR 3.6 1.2 + - - -
1083A THR* 1.3 73.4 - - - +
1085A PHE* 1.3 62.6 + + - +
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Residues in contact with PHE1085 (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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383A VAL* 3.4 34.3 - - + -
384A GLN* 4.6 5.6 - - - -
386A PHE* 4.1 11.4 - - + -
387A PRO* 3.9 17.5 - - + -
635A PHE* 3.6 33.7 - + - -
816A PRO 4.5 1.8 - - - -
817A ILE* 4.3 22.7 - - + -
1003A GLY 4.6 0.4 - - - -
1005A ILE* 4.8 1.8 - - - -
1066A PHE 3.5 16.4 - - - -
1067A THR* 3.2 23.8 + - - +
1068A PRO* 4.1 3.6 - - + -
1083A THR* 2.7 31.7 + - - +
1084A HIS* 1.3 81.5 - + - +
1086A ASP* 1.3 64.1 + - - +
1089A SER* 4.1 9.6 - - - -
1090A ILE* 4.3 7.4 - - + +
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Residues in contact with ASP1086 (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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1003A GLY 3.3 21.1 - - - +
1004A THR* 4.4 4.5 - - - -
1005A ILE* 4.1 19.9 + - + +
1083A THR* 4.7 0.7 - - - -
1084A HIS 4.1 1.0 + - - -
1085A PHE* 1.3 75.1 - - - +
1087A PHE* 1.3 67.5 + - - +
1088A HIS* 3.3 11.6 + - - +
1089A SER* 3.1 35.6 + - - -
1090A ILE* 3.7 6.9 + - - +
16P C 3.6 22.9 + - - +
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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