Contacts of the strand formed by residues 930 - 935 (chain K) in PDB entry 6R90
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 VAL 930 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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922K LEU* 4.0 16.6 - - + -
923K VAL 3.2 8.3 - - - +
928K ARG 3.2 5.7 + - - +
929K SER* 1.3 87.4 - - - +
931K LEU* 1.3 58.0 + - - +
947K ARG* 3.9 2.3 - - - +
948K ASP* 2.7 54.6 + - + +
954K MET* 3.6 11.9 - - + -
957K VAL* 3.5 31.9 - - + -
965K PHE* 5.5 3.4 - - + -
966K LEU 5.0 1.8 - - - +
967K GLY* 4.9 2.2 - - - -
975K PHE* 4.1 12.6 - - + -
977K CYS* 4.8 4.0 - - + -
992K LEU* 4.4 10.8 - - + -
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Residues in contact with LEU 931 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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905K HIS* 4.3 7.0 - - + -
907K ASN 4.4 5.2 - - - +
908K ASN* 3.6 23.6 - - - +
921K ILE 3.5 1.0 - - - +
922K LEU* 3.4 9.3 - - - +
923K VAL* 2.9 44.5 + - + +
928K ARG 5.8 1.1 - - - +
930K VAL* 1.3 75.9 - - - +
932K LEU* 1.3 59.4 + - - +
933K LEU* 3.6 35.6 + - + -
944K GLU* 4.7 4.7 - - + +
946K ALA 3.3 24.5 - - - +
947K ARG* 3.9 37.5 - - + +
992K LEU* 5.4 1.1 - - - -
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Residues in contact with LEU 932 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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920K PHE* 4.1 20.9 - - + -
921K ILE 3.4 17.0 - - - +
922K LEU* 4.7 6.1 - - + +
931K LEU* 1.3 70.3 - - - +
933K LEU* 1.3 70.8 + - - +
945K ILE* 3.2 20.2 + - + +
946K ALA* 2.9 43.1 + - + +
947K ARG* 4.7 0.2 - - - +
959K ILE* 6.5 0.9 - - + -
965K PHE* 4.0 34.8 - - + -
979K LYS* 3.2 35.2 - - + +
992K LEU* 4.8 9.1 - - + +
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Residues in contact with LEU 933 (chain K).
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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888K VAL* 4.7 12.1 - - + -
905K HIS* 3.8 33.2 - - + +
908K ASN* 5.4 0.2 - - - +
920K PHE* 3.6 3.6 - - - -
921K ILE* 2.9 46.7 + - + +
923K VAL* 4.4 17.0 - - + -
931K LEU* 3.6 36.1 - - + -
932K LEU* 1.3 79.8 - - - +
934K ALA* 1.3 63.3 + - - +
942K PHE* 4.8 12.1 - - + -
943K GLU 4.0 5.4 - - - +
944K GLU* 3.9 24.2 - - + +
945K ILE* 4.0 2.5 - - - -
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Residues in contact with ALA 934 (chain K).
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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919K ASP* 3.6 7.4 - - + +
920K PHE* 4.2 14.6 - - + -
933K LEU* 1.3 74.8 - - - +
935K TYR* 1.3 67.3 + - - +
936K LYS* 3.7 8.9 + - + +
942K PHE* 3.4 8.7 - - - -
943K GLU 3.1 30.2 + - - +
945K ILE* 3.3 30.3 - - + -
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Residues in contact with TYR 935 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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876K PHE* 3.6 39.0 - + + -
877K ASN* 5.5 0.2 - - - -
879K LYS* 2.9 22.0 + - - -
890K LEU* 3.6 25.4 - - + -
902K GLU* 2.5 29.0 + - - -
903K CYS* 4.2 2.2 - - - -
919K ASP* 3.0 22.9 + - + +
921K ILE* 4.6 2.5 - - + +
934K ALA* 1.3 73.8 - - - +
936K LYS* 1.3 64.1 + - - +
937K PRO* 3.2 46.1 + - + +
940K GLY* 3.8 18.6 - - - -
941K ASN 4.0 5.8 - - - -
942K PHE* 3.7 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