Contacts of the strand formed by residues 963 - 969 (chain B) in PDB entry 6AHR
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 963 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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700B THR* 4.3 16.4 - - + +
711B LEU* 3.7 27.7 - - + +
715B TRP* 4.3 5.5 + - - -
874B MET* 4.6 12.3 - - + -
875B ILE 3.3 10.8 - - - +
876B CYS* 4.1 11.4 - - - +
955B VAL* 4.6 19.2 - - + +
958B HIS* 6.2 0.7 - - + -
959B CYS* 4.4 17.7 - - + +
961B ARG 3.6 2.5 + - - +
962B THR* 1.3 78.6 - - - +
964B LEU* 1.3 60.5 + - - +
965B GLY 5.1 0.2 - - - +
966B PHE* 4.3 16.4 - - + -
1008B ARG* 4.3 20.9 - - - +
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Residues in contact with LEU 964 (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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711B LEU* 4.4 14.1 - - - +
715B TRP* 4.2 22.7 - - + +
875B ILE* 3.0 31.7 + - + +
876B CYS 4.8 0.4 - - - -
877B VAL* 3.8 24.7 - - + +
962B THR 5.0 0.7 - - - +
963B LEU* 1.3 75.2 - - - +
965B GLY* 1.3 62.4 + - - +
966B PHE* 5.5 1.9 - - - -
984B PHE 4.4 0.3 - - - +
985B VAL* 3.7 6.3 - - + -
986B SER* 3.7 37.8 + - - +
989B GLY* 3.6 34.1 - - - +
990B LEU* 3.8 17.5 - - + +
993B MET* 6.3 0.2 - - + -
1005B VAL* 4.8 4.5 - - + -
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Residues in contact with GLY 965 (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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874B MET* 3.3 2.9 - - - +
875B ILE* 2.8 47.0 + - - +
963B LEU* 3.9 0.4 - - - +
964B LEU* 1.3 81.5 - - - +
966B PHE* 1.3 74.0 + - - -
984B PHE 3.5 6.7 - - - -
985B VAL* 3.7 10.3 - - - -
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Residues in contact with PHE 966 (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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701B LEU 5.9 0.4 - - - -
707B PRO* 3.5 33.9 - - + -
708B TRP* 3.6 50.5 - + + -
711B LEU* 3.6 26.7 - - + -
873B THR 4.0 1.6 - - - -
874B MET* 3.8 28.9 - - + -
955B VAL* 5.4 1.1 - - + -
963B LEU* 4.3 14.4 - - + -
964B LEU 5.7 1.3 - - - -
965B GLY* 1.3 86.7 - - - -
967B VAL* 1.3 59.8 + - - +
968B THR* 4.1 1.5 + - - -
984B PHE* 2.6 51.1 + - + +
985B VAL* 4.8 0.2 - - - +
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Residues in contact with VAL 967 (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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861B LEU* 4.2 9.4 - - + -
870B GLU 4.9 0.7 - - - +
872B HIS* 3.2 31.8 + - - +
873B THR* 3.3 40.6 + - - +
875B ILE* 3.8 20.4 - - + -
966B PHE* 1.3 76.2 - - - +
968B THR* 1.3 62.8 + - - +
969B GLN 3.6 20.2 - - - +
970B GLY* 3.8 9.4 - - - +
981B ALA* 4.1 5.8 - - + -
982B LEU 3.4 14.8 - - - +
983B GLY* 3.7 12.6 - - - -
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Residues in contact with THR 968 (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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662B ASP* 3.7 17.5 + - + +
705B CYS* 6.1 4.5 - - + -
708B TRP* 6.1 6.1 - - + -
871B PRO* 4.1 16.3 - - - +
872B HIS* 4.5 11.2 + - + -
966B PHE* 4.1 1.5 + - + +
967B VAL* 1.3 78.5 - - - +
969B GLN* 1.3 94.2 + - - +
970B GLY 3.7 2.6 + - - -
982B LEU* 3.4 8.7 + - - +
983B GLY* 4.4 0.2 - - - -
984B PHE* 3.6 35.9 - - + -
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Residues in contact with GLN 969 (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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648B ALA* 5.3 3.6 - - + +
651B SER* 5.8 0.2 - - - -
652B GLN* 3.5 37.9 - - + +
656B SER 5.5 1.8 - - - -
657B PRO* 5.0 3.6 - - - +
658B ASN* 2.9 19.5 + - - +
662B ASP* 2.7 41.7 + - - +
871B PRO* 6.0 0.2 - - - -
967B VAL* 3.6 2.6 - - - +
968B THR* 1.3 104.0 + - - +
970B GLY* 1.3 59.8 + - - +
971B ASP 4.0 1.1 + - - -
980B GLU 4.7 0.9 - - - +
981B ALA* 3.6 3.1 - - - -
982B LEU* 3.1 46.4 + - + +
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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