Contacts of the strand formed by residues 984 - 989 (chain A) in PDB entry 4B87
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 ILE 984 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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939A PHE* 3.6 25.5 - - + -
942A LEU* 3.7 41.3 - - + +
943A GLN* 4.2 18.6 - - + +
946A LEU* 3.8 28.9 - - + -
956A ILE* 3.4 26.5 - - + +
980A THR* 3.5 2.6 - - - +
981A LYS 3.0 33.9 + - - +
982A GLY 3.3 0.4 - - - -
983A ASN* 1.4 83.6 - - - +
985A SER* 1.3 68.4 + - - +
986A ILE* 4.3 1.3 - - + -
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Residues in contact with SER 985 (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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955A GLN* 5.6 4.9 + - - -
956A ILE 2.9 11.4 + - - +
957A LEU* 3.6 6.6 - - - -
958A ALA* 2.8 26.2 + - - +
978A PRO* 4.5 4.4 - - - +
979A GLN 3.4 5.2 - - - -
980A THR* 3.2 24.0 + - - +
983A ASN 5.4 0.3 - - - -
984A ILE* 1.3 74.4 + - - +
986A ILE* 1.3 65.3 + - - +
987A TYR* 4.2 21.1 - - - -
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Residues in contact with ILE 986 (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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937A ILE* 4.2 9.6 - - + -
938A ASN* 3.8 30.7 - - - +
939A PHE* 3.9 29.4 - - + +
942A LEU* 3.8 20.4 - - + -
958A ALA 3.4 6.5 - - - +
960A ARG* 3.6 48.1 + - + +
978A PRO* 3.3 1.9 - - - +
979A GLN* 2.9 39.7 + - + +
984A ILE* 4.3 0.4 - - + -
985A SER* 1.3 77.2 - - - +
987A TYR* 1.3 65.9 + - - +
988A GLY 4.0 1.2 + - - -
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Residues in contact with TYR 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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857A PHE* 4.2 23.3 - + - -
861A THR* 3.8 18.2 - - + +
957A LEU* 3.7 43.3 - - + +
958A ALA 2.7 10.0 + - - -
959A PHE* 3.4 23.3 - + + -
960A ARG* 3.0 24.4 + - - +
976A VAL* 4.4 9.6 - - + -
978A PRO* 3.6 45.8 - - + +
985A SER* 4.2 9.6 - - - -
986A ILE* 1.3 76.5 - - - +
988A GLY* 1.3 61.0 + - - +
989A ILE* 3.5 7.1 + - + +
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Residues in contact with GLY 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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960A ARG* 3.2 19.7 - - - +
961A PRO 4.6 1.6 - - - -
962A THR* 3.8 17.6 + - - -
976A VAL* 3.5 24.4 - - - +
977A ILE 5.4 2.0 + - - -
986A ILE* 4.0 3.4 + - - +
987A TYR* 1.3 69.5 - - - +
989A ILE* 1.3 59.2 + - - -
990A PRO* 4.2 0.2 - - - +
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Residues in contact with ILE 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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854A VAL* 3.9 22.9 - - + -
857A PHE* 3.9 27.1 - - + -
858A ALA* 4.4 12.1 - - + -
886A VAL* 4.4 5.6 - - + -
959A PHE* 3.8 36.6 - - + -
960A ARG 2.9 11.6 + - - +
961A PRO* 3.2 4.9 - - - +
962A THR* 2.9 18.0 + - - -
976A VAL* 5.1 1.6 - - + -
987A TYR* 4.1 5.8 - - + +
988A GLY* 1.3 78.1 - - - +
990A PRO* 1.3 64.4 - - + +
991A TYR* 2.9 9.5 + - + -
2042A EDO 3.5 31.4 - - - -
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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