Contacts of the strand formed by residues 1065 - 1069 (chain L) 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 LEU1065 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13L 741 4.6 0.7 - - - -
992L TRP* 3.3 42.8 - - + -
1051L ALA* 3.8 39.0 - - + +
1054L MET* 4.1 20.4 + - + +
1055L LYS* 4.9 4.0 - - + +
1057L PHE 5.3 1.8 + - - -
1063L VAL 4.1 0.6 + - - -
1064L ARG* 1.3 82.5 + - - +
1066L LEU* 1.3 62.6 + - - +
1067L GLY* 3.2 33.0 - - - +
1068L VAL* 4.3 7.4 - - + -
1077L VAL* 3.8 19.5 - - + -
1078L ILE 4.1 4.7 - - - +
1079L MET* 3.8 14.9 - - - +
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Residues in contact with LEU1066 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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992L TRP* 5.0 2.9 - - - -
994L VAL* 4.8 2.9 - - - +
1021L VAL* 3.9 37.1 - - + +
1022L VAL* 3.9 19.1 - - + -
1023L LYS* 6.2 0.2 - - - -
1028L THR* 4.3 10.8 - - + -
1030L VAL* 3.3 33.2 - - + -
1064L ARG* 3.6 30.9 + - + +
1065L LEU* 1.3 74.5 - - - +
1067L GLY* 1.3 57.0 + - - +
1078L ILE* 2.8 22.7 + - + +
1080L GLU* 4.1 24.5 - - + +
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Residues in contact with GLY1067 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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992L TRP* 3.2 17.0 - - - -
994L VAL* 4.4 4.3 - - - -
1065L LEU* 3.2 16.5 - - - +
1066L LEU* 1.3 81.1 - - - +
1068L VAL* 1.3 58.8 + - - +
1077L VAL* 3.6 1.6 - - - +
1078L ILE* 2.6 41.0 + - - +
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Residues in contact with VAL1068 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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984L ALA* 6.0 0.2 - - + -
988L VAL* 4.1 28.5 - - + -
992L TRP* 2.8 23.0 + - + +
993L GLU* 3.2 23.3 - - - -
994L VAL* 3.4 3.5 + - - +
1048L LEU* 5.5 1.6 - - + -
1051L ALA* 5.5 3.6 - - + -
1065L LEU* 4.3 14.1 - - + -
1067L GLY* 1.3 79.0 - - - +
1069L VAL* 1.3 71.2 + - - +
1070L SER* 3.7 14.8 + - - -
1075L THR* 5.0 6.3 - - + -
1076L LEU 3.2 12.6 - - - +
1077L VAL* 4.2 15.3 - - + +
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Residues in contact with VAL1069 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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994L VAL* 3.6 24.5 - - + +
996L ARG* 3.3 44.8 + - + +
999L ILE* 3.8 12.6 - - + -
1068L VAL* 1.3 72.9 - - - +
1070L SER* 1.3 58.5 + - - +
1071L GLN* 4.2 6.7 - - + +
1075L THR* 3.6 8.3 - - - +
1076L LEU* 2.7 50.6 + - + +
1078L ILE* 3.6 23.1 - - + -
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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