Contacts of the strand formed by residues 1075 - 1080 (chain R) 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 THR1075 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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982R SER* 5.0 1.2 + - - -
984R ALA* 3.6 28.0 - - + +
996R ARG* 4.7 0.2 - - - +
1033R LYS 3.5 3.1 - - - +
1034R THR* 3.5 2.3 - - - -
1035R VAL* 3.1 45.4 + - + +
1044R ARG* 3.7 18.5 + - - -
1048R LEU* 4.5 16.2 - - + -
1068R VAL* 4.1 11.9 - - + -
1069R VAL 3.6 13.2 - - - +
1070R SER* 5.1 1.4 + - - +
1072R GLY 4.8 3.8 + - - -
1073R GLN 3.8 3.1 + - - -
1074R PRO* 1.3 73.0 - - - +
1076R LEU* 1.3 69.0 + - - +
1077R VAL* 4.7 5.2 - - + -
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Residues in contact with LEU1076 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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996R ARG* 4.1 19.5 - - + +
999R ILE* 3.8 33.4 - - + -
1001R MET* 4.3 7.2 - - + -
1032R ILE* 4.1 13.0 - - + -
1033R LYS 3.4 2.7 - - - +
1034R THR* 3.5 32.3 - - + -
1068R VAL* 3.1 9.4 - - - +
1069R VAL* 2.7 55.2 + - + -
1074R PRO* 3.3 15.9 + - + +
1075R THR* 1.3 78.2 - - - +
1077R VAL* 1.3 61.4 + - - +
1078R ILE* 5.0 1.6 - - + -
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Residues in contact with VAL1077 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14R 741 3.1 43.7 - - + +
1032R ILE* 3.4 4.2 - - - -
1033R LYS* 3.1 18.9 + - + +
1035R VAL* 4.8 0.9 - - + -
1047R PHE* 3.0 42.4 - - + -
1048R LEU* 5.1 1.8 - - + -
1051R ALA* 4.9 6.5 - - + -
1065R LEU* 4.3 20.4 - - + -
1067R GLY 3.9 7.2 - - - +
1068R VAL* 4.2 9.2 - - + -
1075R THR* 4.7 5.6 - - + -
1076R LEU* 1.3 76.9 - - - +
1078R ILE* 1.3 67.1 + - - +
1079R MET* 4.8 0.9 - - + -
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Residues in contact with ILE1078 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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994R VAL* 3.5 32.3 - - + -
999R ILE* 3.5 30.3 - - + -
1018R ALA* 4.3 6.5 - - + -
1021R VAL* 5.4 2.5 - - + -
1030R VAL* 3.5 40.4 - - + -
1031R ALA 3.7 3.1 - - - +
1032R ILE* 4.5 9.9 - - + -
1065R LEU* 3.7 4.9 - - - +
1066R LEU* 2.7 42.1 + - + -
1067R GLY* 2.8 21.0 + - - +
1068R VAL* 4.9 0.4 - - - -
1069R VAL* 4.2 6.5 - - + +
1076R LEU* 4.9 1.8 - - + +
1077R VAL* 1.3 76.2 - - - +
1079R MET* 1.3 56.2 + - - +
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Residues in contact with MET1079 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14R 741 2.8 81.2 - - + +
1030R VAL* 3.4 9.7 - - - +
1031R ALA 3.0 28.8 + - - +
1054R MET* 4.5 13.0 - - + +
1063R VAL* 3.5 25.6 - - + +
1064R ARG 3.1 23.6 - - - +
1065R LEU* 3.7 22.4 - - - +
1066R LEU* 4.3 4.5 - - - +
1077R VAL* 3.8 2.2 + - + -
1078R ILE* 1.3 73.1 - - - +
1080R GLU* 1.3 64.6 + - - +
1152R GLY 5.1 4.3 - - - +
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Residues in contact with GLU1080 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14R 741 3.5 16.1 - - - -
1029R ARG 4.7 2.2 - - - -
1031R ALA 4.4 0.2 - - - -
1062R VAL 3.9 1.6 - - - +
1063R VAL* 3.7 10.7 - - - +
1064R ARG* 2.9 47.6 + - + +
1066R LEU* 4.0 18.5 - - + +
1079R MET* 1.3 76.8 - - - +
1081R LEU* 1.3 70.9 + - - +
1082R MET* 3.8 11.3 + - - +
1144R ALA* 5.5 1.0 - - - +
1150R LYS* 2.6 35.5 + - - +
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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