Contacts of the strand formed by residues 1075 - 1080 (chain S) 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 S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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982S SER* 4.7 2.3 + - - -
984S ALA* 3.7 26.3 - - + +
996S ARG* 4.6 0.9 - - - +
1033S LYS 3.4 3.6 - - - +
1035S VAL* 3.0 43.5 + - - +
1044S ARG* 3.6 16.8 + - - -
1047S PHE* 4.6 8.7 - - + -
1048S LEU* 4.5 15.0 - - + -
1068S VAL* 4.4 8.5 - - + -
1069S VAL 3.7 14.4 - - - +
1070S SER* 5.4 1.2 + - - +
1072S GLY 4.7 4.4 + - - -
1073S GLN 3.4 5.4 + - - -
1074S PRO* 1.3 71.4 - - - +
1076S LEU* 1.3 70.7 + - - +
1077S VAL* 5.1 0.2 - - + -
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Residues in contact with LEU1076 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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996S ARG* 4.0 19.1 - - + +
999S ILE* 4.4 17.3 - - + -
1001S MET* 4.5 8.1 - - + -
1032S ILE* 4.1 20.0 - - + -
1033S LYS 3.2 3.4 - - - +
1034S THR* 3.4 32.8 - - + -
1068S VAL* 3.1 9.4 - - - +
1069S VAL* 2.8 58.8 + - + -
1074S PRO* 3.4 20.9 - - + +
1075S THR* 1.3 74.8 - - - +
1077S VAL* 1.3 62.1 + - - +
1078S ILE* 4.1 3.1 - - + -
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Residues in contact with VAL1077 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15S 741 2.8 47.3 - - - +
1032S ILE* 3.5 2.2 - - - -
1033S LYS* 3.0 19.5 + - + -
1047S PHE* 3.0 40.8 - - + -
1048S LEU* 4.9 4.7 - - + -
1051S ALA* 5.0 5.2 - - + -
1065S LEU* 4.3 20.4 - - + -
1067S GLY 3.9 3.8 - - - +
1068S VAL* 4.2 13.0 - - + -
1075S THR* 4.3 0.9 + - + -
1076S LEU* 1.3 77.1 - - - +
1078S ILE* 1.3 62.6 + - - +
1079S MET* 4.1 12.1 - - + -
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Residues in contact with ILE1078 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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994S VAL* 4.5 4.0 - - + -
999S ILE* 3.7 32.3 - - + -
1018S ALA* 4.6 5.4 - - + -
1021S VAL* 5.3 1.6 - - + -
1030S VAL* 3.5 32.8 - - + -
1031S ALA 3.5 2.7 - - - -
1032S ILE* 4.1 14.8 - - + -
1065S LEU* 3.7 4.3 - - - +
1066S LEU* 2.8 43.4 + - + -
1067S GLY 2.8 26.2 + - - +
1069S VAL* 3.8 26.5 - - + +
1076S LEU* 4.3 6.3 - - + -
1077S VAL* 1.3 74.3 - - - +
1079S MET* 1.3 62.5 + - - +
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Residues in contact with MET1079 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15S 741 3.0 93.1 - - + +
1030S VAL* 3.4 6.9 - - - +
1031S ALA 2.9 25.9 + - - +
1054S MET* 4.6 8.5 - - - +
1063S VAL* 4.0 25.8 - - + +
1064S ARG 3.5 8.1 - - - +
1065S LEU* 3.5 35.0 - - - +
1066S LEU* 4.2 4.3 - - - -
1077S VAL* 3.8 2.7 + - + -
1078S ILE* 1.3 76.3 - - - +
1080S GLU* 1.3 66.1 + - - +
1081S LEU 3.3 0.3 + - - -
1152S GLY 5.1 5.8 - - - +
1154S PHE* 6.3 0.2 - - + -
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Residues in contact with GLU1080 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15S 741 3.5 15.6 - - - -
1029S ARG 4.9 0.7 - - - -
1063S VAL* 3.7 9.9 - - + +
1064S ARG* 2.8 48.9 + - + +
1066S LEU* 3.9 18.4 - - + +
1079S MET* 1.3 72.7 - - - +
1081S LEU* 1.3 71.2 + - - +
1082S MET* 3.2 9.7 - - - +
1144S ALA* 5.4 0.7 - - - +
1150S LYS* 2.6 45.5 + - - +
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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