Contacts of the strand formed by residues 1044 - 1056 (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 LYS1044 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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350A PRO 2.8 19.4 + - - +
351A MET* 3.6 33.7 + - + +
353A GLN* 3.5 19.9 + - + +
354A MET* 2.9 30.1 + - - +
382A VAL* 4.0 17.4 - - - +
384A GLN* 3.0 27.6 + - - +
642A HIS* 5.8 1.0 + - - -
1005A ILE* 3.8 15.9 - - + -
1006A GLY 3.6 4.7 - - - -
1007A THR* 4.2 4.3 - - - -
1042A GLY 3.6 1.8 + - - -
1043A VAL* 1.3 71.4 - - - +
1045A ARG* 1.3 61.7 + - - +
1046A THR 3.8 11.4 - - - +
1047A THR* 3.7 28.5 - - - +
1070A GLN* 5.5 0.4 + - - -
1084A HIS* 5.3 0.4 - - - -
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Residues in contact with ARG1045 (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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353A GLN* 3.4 26.3 + - - +
354A MET* 3.5 29.3 - - + +
1006A GLY 2.6 15.7 + - - +
1007A THR 5.0 1.3 - - - -
1008A VAL* 4.4 6.6 - - + +
1012A THR* 3.3 31.5 + - - +
1016A PHE* 4.1 19.4 - - - -
1043A VAL 3.6 0.4 + - - -
1044A LYS* 1.3 74.1 - - - +
1046A THR* 1.3 78.6 + - + +
13P C 6.3 0.2 - - - -
12T C 4.1 9.0 + - - -
13T C 3.3 32.4 + - - -
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Residues in contact with THR1046 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A GLN* 4.9 2.9 - - - -
1005A ILE* 3.7 1.9 - - - -
1006A GLY* 2.7 40.0 + - - +
1044A LYS* 3.8 10.8 - - - +
1045A ARG* 1.3 100.4 - - + +
1047A THR* 1.3 72.7 + - - +
11T C 4.6 4.4 - - - +
12T C 3.5 37.7 - - - +
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Residues in contact with THR1047 (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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384A GLN* 4.2 12.6 - - - +
1004A THR 3.3 13.7 - - - +
1005A ILE* 4.6 1.3 - - + -
1006A GLY 4.4 1.6 - - - +
1044A LYS* 3.7 25.1 - - - +
1046A THR* 1.3 84.7 - - - +
1048A GLY* 1.3 58.9 + - - +
1070A GLN* 3.5 26.6 + - - +
1072A PRO* 4.9 0.4 - - - -
1073A ALA* 2.9 41.8 + - - +
1074A ASP* 5.0 2.8 + - - -
11T C 3.7 16.7 - - - +
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Residues in contact with GLY1048 (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* 3.7 6.2 - - - -
1004A THR* 3.0 34.1 + - - +
1047A THR* 1.3 76.6 - - - +
1049A GLN* 1.3 63.3 + - - +
1072A PRO* 3.6 16.0 - - - +
1073A ALA 4.3 0.4 - - - +
1082A THR* 4.0 1.7 + - - +
11T C 3.7 16.8 - - - -
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Residues in contact with GLN1049 (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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1001A ARG* 3.0 35.4 + - + +
1002A ALA 4.0 3.8 - - - -
1004A THR* 3.6 9.3 + - - +
1048A GLY* 1.3 72.3 - - - -
1050A HIS* 1.3 73.3 + - - +
1051A PRO* 3.4 3.1 - - - +
1072A PRO* 3.4 31.6 - - + +
1078A SER* 5.0 4.3 + - - -
1080A TRP* 5.2 5.8 - - - +
1082A THR* 4.4 6.1 - - + -
9T T 5.5 1.0 - - - +
10T G 3.6 35.3 + - - +
11T C 2.6 26.9 + - - +
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Residues in contact with HIS1050 (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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1001A ARG* 2.8 28.8 + - - +
1002A ALA* 2.9 46.9 + - + +
1003A GLY 5.0 0.7 - - - +
1004A THR* 3.5 12.6 - - + +
1049A GLN* 1.3 71.0 - - - +
1051A PRO* 1.3 69.3 - - + +
1052A GLY 3.1 12.6 + - - +
1053A GLY* 2.8 29.5 + - - +
1087A PHE* 4.2 12.1 - - + -
1096A LYS* 4.0 4.0 + - + +
1098A ASP* 3.4 17.0 - - - -
1100A LEU* 5.0 0.4 - - + -
16P C 3.0 19.9 + - - -
17P C 2.7 38.2 + - - -
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Residues in contact with PRO1051 (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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983A GLN* 3.0 19.1 + - - -
1001A ARG* 3.7 7.0 + - - +
1004A THR* 5.2 0.4 - - + -
1049A GLN 4.1 4.3 - - - +
1050A HIS* 1.3 97.0 - - + +
1052A GLY* 1.3 54.9 + - - -
1100A LEU* 4.3 11.0 - - + +
1101A GLY 4.9 0.2 + - - -
15P A 4.1 19.7 - - + +
16P C 3.7 35.2 - - - +
17P C 5.5 2.2 - - - +
8T T 4.4 7.0 - - - +
9T T 3.7 35.1 - - - +
10T G 5.0 0.7 - - - -
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Residues in contact with GLY1052 (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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983A GLN* 3.8 2.7 - - - -
987A HIS* 3.1 26.2 + - - -
1001A ARG* 4.1 2.2 - - - -
1050A HIS* 3.0 7.4 + - - -
1051A PRO* 1.3 81.0 - - - +
1053A GLY* 1.3 66.2 + - - +
1054A ILE 3.4 1.7 + - - -
1097A LEU 3.4 0.3 - - - +
1098A ASP* 4.2 1.8 - - - -
1099A ILE* 3.2 32.1 + - - +
1100A LEU* 4.0 6.2 - - - +
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Residues in contact with GLY1053 (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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1001A ARG* 3.7 2.8 - - - -
1002A ALA* 3.1 27.8 + - - +
1050A HIS* 2.8 25.9 + - - +
1052A GLY* 1.3 71.6 - - - +
1054A ILE* 1.3 66.6 + - - +
1055A ILE 4.0 0.7 - - - -
1096A LYS* 3.9 10.8 - - - -
1097A LEU 3.3 7.6 - - - -
1098A ASP* 3.4 13.0 + - - -
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Residues in contact with ILE1054 (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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987A HIS* 3.7 28.3 - - + -
990A THR* 3.7 15.9 - - + +
999A VAL* 3.6 33.7 - - + -
1000A TYR 3.7 2.5 - - - +
1001A ARG* 3.9 28.0 - - - -
1052A GLY 4.0 1.1 - - - +
1053A GLY* 1.3 81.2 - - - +
1055A ILE* 1.3 65.0 + - - +
1056A VAL* 3.8 6.2 + - + +
1080A TRP* 4.0 17.5 - - + -
1096A LYS* 3.4 3.0 - - - -
1097A LEU* 2.8 43.5 + - + +
1099A ILE* 4.2 9.0 - - + -
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Residues in contact with ILE1055 (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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998A ASN 4.5 0.2 - - - -
999A VAL* 3.4 5.9 - - - -
1000A TYR* 2.9 37.1 + - + +
1002A ALA* 4.0 24.2 - - + +
1054A ILE* 1.3 71.2 - - - +
1056A VAL* 1.3 63.8 + - - +
1057A VAL* 3.8 4.9 + - + +
1063A ILE* 5.1 1.3 - - + -
1083A THR* 4.3 15.0 - - + -
1087A PHE* 3.7 31.4 - - + -
1090A ILE* 4.5 12.3 - - + -
1094A LEU* 3.5 37.9 - - + +
1095A LEU 3.8 3.1 - - - +
1096A LYS* 4.2 15.5 - - + -
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Residues in contact with VAL1056 (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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822A TYR 5.1 0.2 - - - +
824A PRO* 4.0 31.9 - - + -
872A ILE* 4.8 5.4 - - + -
994A PHE* 4.2 26.0 - - + -
998A ASN 3.6 5.6 - - - +
999A VAL* 4.6 3.8 - - + -
1054A ILE 3.9 10.3 - - - +
1055A ILE* 1.3 75.5 - - - +
1057A VAL* 1.3 60.8 + - - +
1058A PRO* 3.4 2.3 - - - +
1094A LEU* 3.4 22.4 - - - +
1095A LEU* 3.0 29.4 + - + +
1097A LEU* 4.2 24.5 - - + -
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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