Contacts of the strand formed by residues 1029 - 1035 (chain D) in PDB entry 3F5P
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 ARG1029 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1015D GLU* 2.7 39.3 + - - -
1016D GLY 3.4 8.7 - - - +
1017D VAL* 4.7 7.2 - - + +
1028D THR* 1.3 88.1 - - - +
1030D VAL* 1.3 60.2 - - - +
1081D LEU* 3.5 37.6 + - + +
1083D THR* 3.9 18.7 - - - +
1145D GLU* 4.2 12.1 + - - -
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Residues in contact with VAL1030 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1015D GLU* 3.6 3.6 - - - -
1016D GLY 3.0 31.6 + - - +
1017D VAL 4.0 0.4 - - - -
1018D ALA* 3.7 29.2 - - + +
1028D THR* 3.8 9.2 - - + +
1029D ARG* 1.3 80.3 - - - +
1031D ALA* 1.3 59.3 + - - +
1032D ILE* 3.3 27.1 - - + -
1066D LEU* 3.4 33.0 - - + -
1078D ILE* 3.5 11.4 - - + -
1079D MET 3.4 9.9 - - - +
1080D GLU* 5.0 0.2 - - - -
1081D LEU* 3.7 12.6 - - - +
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Residues in contact with ALA1031 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D 741 3.6 52.6 - - + +
1005D LEU* 4.5 1.1 - - + -
1013D VAL* 4.2 5.4 - - + -
1014D TYR 3.2 8.7 - - - +
1015D GLU* 4.6 0.9 - - - +
1030D VAL* 1.3 73.6 - - - +
1032D ILE* 1.3 60.4 + - - +
1078D ILE* 3.5 4.9 - - - -
1079D MET 2.9 34.6 + - - +
1080D GLU 4.1 0.6 + - - +
1081D LEU* 4.0 6.2 - - + +
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Residues in contact with ILE1032 (chain D).
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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4D 741 4.1 1.1 - - - -
999D ILE* 3.7 20.9 - - + -
1000D THR 5.0 2.9 - - - +
1001D MET* 4.2 18.6 - - + -
1013D VAL* 3.3 2.0 - - - -
1014D TYR* 2.6 56.7 + - + +
1016D GLY* 4.5 6.7 - - - +
1017D VAL 5.0 0.2 - - - +
1030D VAL* 3.3 35.0 - - + +
1031D ALA* 1.3 75.0 - - - +
1033D LYS* 1.3 62.9 + - - +
1076D LEU* 3.8 38.1 - - + -
1077D VAL 3.5 7.0 - - - +
1078D ILE* 3.8 9.2 - - + -
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Residues in contact with LYS1033 (chain D).
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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4D 741 3.0 51.0 + - + +
1008D GLY* 3.6 5.3 - - - -
1009D SER* 2.7 45.7 + - - +
1010D PHE 3.2 6.2 - - - +
1011D GLY 4.1 11.0 - - - +
1012D MET 3.3 8.7 - - - +
1013D VAL* 3.7 21.5 - - + +
1032D ILE* 1.3 74.7 - - - +
1034D THR* 1.3 74.4 + - - +
1035D VAL* 5.3 0.2 - - + -
1047D PHE* 3.8 15.3 - - + -
1075D THR 3.4 1.0 - - - +
1076D LEU* 3.4 7.8 - - - +
1077D VAL* 3.0 33.3 + - + +
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Residues in contact with THR1034 (chain D).
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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1001D MET* 3.8 26.0 - - + -
1011D GLY* 3.4 23.0 - - - -
1012D MET* 3.0 12.5 + - - +
1014D TYR* 3.4 19.1 + - + -
1032D ILE* 5.0 0.2 - - + -
1033D LYS* 1.3 73.9 - - - +
1035D VAL* 1.3 63.3 + - - +
1036D ASN 3.9 2.1 + - - -
1074D PRO* 4.3 15.5 - - + -
1075D THR 3.4 4.3 - - - -
1076D LEU* 3.3 28.3 - - + -
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Residues in contact with VAL1035 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1010D PHE* 3.3 32.1 - - + +
1033D LYS* 4.9 1.6 - - + +
1034D THR* 1.3 74.8 - - - +
1036D ASN* 1.3 67.1 + - - +
1039D ALA* 4.4 17.0 - - + -
1044D ARG* 4.4 18.6 + - + +
1047D PHE* 3.5 37.9 - - + -
1073D GLN 4.3 0.9 - - - +
1074D PRO* 3.6 5.0 - - - +
1075D THR* 3.0 45.2 + - - +
1077D VAL* 4.8 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