Contacts of the strand formed by residues 964 - 969 (chain K) in PDB entry 6R8Y
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 ASN 964 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1K MET* 5.3 8.1 - - - +
2K SER* 2.6 39.3 + - - +
960K LEU* 3.0 43.5 + - + -
961K ASP* 2.7 40.5 + - - +
963K ASP* 1.3 91.5 - - - +
965K PHE* 1.3 64.5 + - - +
976K VAL* 4.5 3.4 - - + +
977K CYS 3.6 4.3 - - - +
978K GLN* 4.6 4.9 - - - +
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Residues in contact with PHE 965 (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* 6.3 0.9 - - + -
922K LEU* 3.7 36.3 - - + -
930K VAL* 5.9 2.5 - - + -
932K LEU* 3.4 45.1 - - + -
958K GLU 3.6 3.4 - - - -
959K ILE* 4.7 9.0 - - + -
960K LEU* 5.1 0.4 - - - -
961K ASP 4.0 5.4 - - - -
962K ASP* 3.5 24.2 - - - -
963K ASP 3.6 15.5 - - - -
964K ASN* 1.3 81.5 - - - +
966K LEU* 1.3 61.4 + - - +
967K GLY 4.1 0.2 + - - -
975K PHE* 3.9 1.9 - - - +
976K VAL* 3.4 6.0 - - - +
977K CYS* 2.8 59.5 + - + +
978K GLN* 4.5 0.2 - - - -
979K LYS* 4.1 7.4 - - - -
992K LEU* 4.3 13.9 - - + -
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Residues in contact with LEU 966 (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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922K LEU* 4.7 1.2 - - - +
957K VAL* 3.2 6.1 - - - +
958K GLU* 2.7 47.9 + - + +
960K LEU* 4.3 28.2 - - + +
964K ASN 4.3 0.4 - - - -
965K PHE* 1.3 73.4 - - - +
967K GLY* 1.3 66.3 + - - +
974K LEU* 4.4 15.5 - - + -
975K PHE* 3.3 18.4 - - - +
976K VAL* 4.0 15.0 - - + +
1007K PHE* 3.5 37.5 - - + -
1028K VAL* 5.1 2.0 - - + -
1040K VAL* 4.4 19.5 - - + -
1088K PHE* 4.5 6.7 - - + -
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Residues in contact with GLY 967 (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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930K VAL* 5.4 0.7 - - - -
954K MET* 3.4 19.1 - - - -
956K ALA 3.5 4.0 - - - -
957K VAL* 4.3 1.3 - - - -
965K PHE 4.1 0.2 + - - -
966K LEU* 1.3 76.9 - - - +
968K ALA* 1.3 60.5 + - - -
974K LEU* 3.2 9.8 - - - +
975K PHE* 2.9 47.8 + - - +
1007K PHE* 4.8 0.9 - - - -
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Residues in contact with ALA 968 (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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954K MET* 3.0 11.3 - - - +
955K SER* 2.9 27.2 + - - +
956K ALA 2.9 12.8 + - - +
967K GLY* 1.3 71.4 - - - -
969K GLU* 1.3 62.6 + - - +
973K ASN 3.3 7.0 - - - +
974K LEU* 3.3 22.4 - - + -
975K PHE* 4.7 0.4 - - - -
1002K GLU 6.0 0.4 - - - +
1004K VAL* 3.7 27.6 - - + +
1007K PHE* 4.2 4.3 - - + -
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Residues in contact with GLU 969 (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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952K ASN* 4.0 20.8 + - + +
953K TRP* 3.1 25.4 + - - +
954K MET* 4.2 8.1 - - - -
955K SER* 4.0 6.8 + - - +
968K ALA* 1.3 76.5 - - - +
970K ASN* 1.3 61.8 + - - +
971K ALA* 2.5 32.1 + - - +
972K PHE* 2.9 23.7 + - - -
973K ASN* 2.5 57.0 + - + +
975K PHE* 4.9 6.1 - - + -
1002K GLU 5.2 1.0 - - - +
1003K PHE* 5.1 3.5 - - - -
1004K VAL 5.7 0.3 + - - -
1076K PHE* 5.7 1.1 - - + -
1078K THR* 4.2 9.3 - - - +
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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