Contacts of the strand formed by residues 986 - 991 (chain A) in PDB entry 3LYI
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 LEU 986 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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975A GLY 4.8 0.9 - - - +
978A MET* 3.7 48.0 - - + +
979A GLN* 2.9 22.6 + - + +
982A SER* 3.8 21.3 - - - +
985A LYS* 1.3 90.8 - - - +
987A PHE* 1.3 62.2 + - - +
1000A TRP* 3.9 34.9 - - + +
1001A LEU* 3.6 6.3 - - - +
1002A PRO* 3.5 32.5 - - + -
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Residues in contact with PHE 987 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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947A ILE* 4.6 17.7 - - + -
985A LYS* 3.5 52.0 - - + -
986A LEU* 1.3 76.1 - - - +
988A LEU* 1.3 63.7 + - - +
989A VAL 3.6 0.3 + - - -
999A GLN 3.6 0.9 - - - +
1000A TRP* 3.3 7.2 - - - -
1001A LEU 2.7 35.0 + - - +
1003A LYS* 3.6 54.1 - - + -
1006A MET* 4.2 14.3 - - + +
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Residues in contact with LEU 988 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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947A ILE* 3.4 7.3 - - - +
948A ILE* 2.9 43.5 + - + +
950A PRO* 3.9 15.0 - - + +
967A PRO* 3.6 35.9 - - + -
971A VAL* 3.6 24.7 - - + -
987A PHE* 1.3 73.9 - - - +
989A VAL* 1.3 60.0 + - - +
998A TRP* 3.6 24.5 - - + -
999A GLN 3.7 13.7 - - - +
1000A TRP* 3.6 36.3 - - + +
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Residues in contact with VAL 989 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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933A VAL* 4.4 4.0 - - + -
935A ALA* 4.5 1.1 - - + -
945A ALA* 3.8 15.3 - - + -
946A LEU 3.2 6.7 - - - +
947A ILE* 3.7 17.7 - - + +
987A PHE 5.1 0.2 - - - +
988A LEU* 1.3 77.8 - - - +
990A LEU* 1.3 59.7 + - - +
991A PHE* 3.7 31.0 - - + -
997A SER 3.8 0.2 - - - +
998A TRP* 3.3 13.3 - - - -
999A GLN 2.8 42.6 + - - +
1001A LEU* 4.2 13.7 - - + -
1006A MET* 3.6 28.9 - - + -
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Residues in contact with LEU 990 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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945A ALA* 3.4 1.0 - - - -
946A LEU* 2.8 45.7 + - + +
948A ILE* 4.1 8.7 - - + +
965A PRO* 3.5 39.3 - - + -
989A VAL* 1.3 72.9 - - - +
991A PHE* 1.3 66.1 + - - +
992A PHE* 3.8 1.7 + - - -
996A ARG* 3.5 35.7 - - + +
997A SER 3.5 14.8 - - - +
998A TRP* 3.8 30.5 - - + +
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Residues in contact with PHE 991 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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935A ALA* 3.8 33.0 - - + -
937A CYS* 3.6 22.4 - - - -
943A TYR* 3.7 21.5 - + + -
944A PRO 3.6 9.9 - - - +
945A ALA* 3.6 10.1 - - + -
989A VAL* 3.7 25.6 - - + -
990A LEU* 1.3 79.7 - - - +
992A PHE* 1.3 58.4 + - - +
993A ASP* 3.1 30.8 + - - +
996A ARG* 3.7 13.7 - - - +
997A SER 2.8 23.3 + - - +
999A GLN* 3.7 18.6 - - + -
1001A LEU* 4.2 1.1 - - + -
1500A OCS 3.8 24.7 - - - +
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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