Contacts of the strand formed by residues 1012 - 1018 (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 MET1012 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1094H LEU* 4.4 22.7 - - + +
1105H ALA* 4.1 14.2 - - + +
1106H PRO 3.9 15.9 - - - +
1107H PRO* 3.9 21.3 - - + -
1208H LEU* 4.8 0.9 - - + -
1004R GLU* 3.5 27.4 - - + +
1006R GLY* 3.5 21.3 - - - +
1007R GLN* 3.9 18.8 - - - +
1008R GLY 4.3 0.2 - - - +
1011R GLY* 1.3 72.8 - - - -
1013R VAL* 1.3 64.1 + - - +
1014R TYR* 3.5 27.7 - - + -
1032R ILE 3.6 1.4 - - - +
1033R LYS* 3.4 1.1 - - - -
1034R THR* 3.0 37.6 + - - +
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Residues in contact with VAL1013 (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 3.4 56.1 - - + +
1004R GLU* 3.5 4.9 - - - +
1005R LEU* 2.7 35.2 + - + -
1006R GLY 3.0 18.3 + - - +
1007R GLN 4.5 1.1 - - - +
1008R GLY* 3.8 19.1 - - - +
1012R MET* 1.3 73.7 - - - +
1014R TYR* 1.3 66.0 + - - +
1031R ALA* 4.2 2.5 - - + -
1032R ILE 3.5 4.9 - - - +
1033R LYS* 3.7 25.1 - - + -
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Residues in contact with TYR1014 (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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1107H PRO* 3.2 3.6 - - - +
1108H SER* 2.8 33.8 + - - -
1111H LYS* 3.4 32.8 - - - +
1001R MET* 3.9 35.0 - - + -
1003R ARG* 3.7 8.7 - - - -
1004R GLU* 2.9 45.7 + - - -
1005R LEU* 3.6 5.9 - - - +
1012R MET* 3.5 29.2 - - + -
1013R VAL* 1.3 78.6 - - - +
1015R GLU* 1.3 64.0 + - - +
1031R ALA* 3.3 5.4 - - - +
1032R ILE* 2.6 46.1 + - + +
1034R THR* 4.1 7.2 - - + -
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Residues in contact with GLU1015 (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 5.8 0.5 - - - +
1001R MET* 3.5 3.3 - - - -
1002R SER* 2.8 36.3 + - - +
1003R ARG* 3.0 27.5 + - + +
1005R LEU* 3.5 27.2 - - + +
1014R TYR* 1.3 77.2 - - - +
1016R GLY* 1.3 66.2 + - - +
1029R ARG* 2.7 36.2 + - - -
1030R VAL 3.6 8.5 - - - +
1032R ILE* 4.6 1.1 - - - -
1081R LEU* 4.0 12.4 - - + +
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Residues in contact with GLY1016 (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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1000R THR* 3.0 14.1 - - - -
1001R MET* 4.1 1.6 - - - -
1002R SER* 4.3 4.5 - - - -
1015R GLU* 1.3 83.8 - - - +
1017R VAL* 1.3 64.9 + - - +
1029R ARG* 3.6 5.4 - - - +
1030R VAL* 2.8 36.4 + - - +
1032R ILE* 4.2 6.7 - - - +
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Residues in contact with VAL1017 (chain R).
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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998R LYS 3.8 0.3 - - - +
999R ILE* 3.7 1.9 - - - +
1000R THR* 2.8 48.1 + - + +
1016R GLY* 1.3 77.2 - - - +
1018R ALA* 1.3 65.0 + - - +
1019R LYS* 3.8 7.7 + - + +
1027R GLU* 3.7 42.2 - - + +
1028R THR 3.3 9.9 - - - +
1029R ARG* 4.8 10.8 - - + +
1030R VAL* 3.8 2.0 - - - -
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Residues in contact with ALA1018 (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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998R LYS 3.5 4.7 - - - -
999R ILE* 3.4 17.3 - - + -
1017R VAL* 1.3 73.0 - - - +
1019R LYS* 1.3 65.9 + - - +
1020R GLY 3.4 2.6 + - - -
1021R VAL* 3.4 28.7 + - + +
1028R THR* 2.8 28.5 + - - +
1030R VAL* 3.5 25.5 - - + +
1078R ILE* 4.3 3.1 - - + -
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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