Contacts of the strand formed by residues 998 - 1002 (chain B) 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 TRP 998 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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948B ILE* 4.2 14.4 - - + -
965B PRO* 3.2 29.4 - - + -
966B ALA 3.9 4.0 - - - -
967B PRO* 3.5 24.9 - - + -
968B PRO* 3.6 27.2 - - + +
971B VAL* 3.8 34.8 - - + +
988B LEU* 4.0 21.3 - - + -
989B VAL 3.3 10.8 - - - +
990B LEU* 3.5 33.9 - - + -
991B PHE* 4.5 1.8 - - - -
996B ARG* 3.4 14.9 + - + +
997B SER* 1.3 76.6 - - - +
999B GLN* 1.3 72.7 + - - +
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Residues in contact with GLN 999 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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937B CYS* 4.7 14.6 - - - -
974B ILE* 4.7 7.9 - - - +
978B MET* 3.4 36.0 - - - +
987B PHE 3.6 0.2 - - - +
988B LEU* 3.5 4.1 - - - +
989B VAL* 2.9 37.7 + - + +
991B PHE* 4.2 15.8 - - + -
998B TRP* 1.3 79.8 + - - +
1000B TRP* 1.3 88.7 + - - +
1001B LEU* 4.1 3.7 - - + +
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Residues in contact with TRP1000 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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950B PRO* 3.7 30.7 - - + -
971B VAL* 2.8 29.5 + - + +
972B LEU* 4.1 15.9 - - + -
974B ILE* 4.6 1.3 - - + -
975B GLY* 3.5 27.9 - - - -
978B MET* 3.6 21.6 - - + +
979B GLN* 5.4 2.2 - - - -
986B LEU* 3.8 42.3 - - + +
987B PHE* 3.2 19.3 - - - -
988B LEU* 3.7 45.0 - - + +
999B GLN* 1.3 95.3 + - - +
1001B LEU* 1.3 68.3 + - - +
1002B PRO* 4.6 0.3 - - - +
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Residues in contact with LEU1001 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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935B ALA* 3.6 30.7 - - + -
936B LYS 3.4 28.9 - - - +
937B CYS* 4.1 21.1 - - + -
986B LEU* 3.9 3.1 - - - -
987B PHE* 2.7 42.7 + - - +
989B VAL* 4.2 13.7 - - + -
999B GLN* 4.1 3.1 - - + +
1000B TRP* 1.3 80.9 - - - +
1002B PRO* 1.3 76.3 - - + +
1005B LYS* 4.0 14.6 - - + +
1006B MET* 3.9 8.8 - - + +
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Residues in contact with PRO1002 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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984B GLU* 3.3 31.2 - - + +
985B LYS 3.4 11.2 - - - +
986B LEU* 3.8 16.3 - - + -
1000B TRP 4.6 0.2 - - - +
1001B LEU* 1.3 92.7 - - + +
1003B LYS* 1.3 66.9 + - - +
1004B SER* 3.7 8.3 - - - +
1005B LYS* 2.9 40.7 + - + +
1006B MET* 3.7 5.6 - - - +
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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