Contacts of the helix formed by residues 68 - 78 (chain L) in PDB entry 6R92
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 SER 68 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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837K TYR 5.6 1.2 + - - -
67L ARG* 1.3 87.0 + - - +
69L ILE* 1.3 57.3 + - - +
70L VAL 3.5 1.3 - - - -
71L ARG* 3.6 41.8 - - - +
72L THR* 2.5 54.4 + - - +
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Residues in contact with ILE 69 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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837K TYR 5.4 2.5 - - - +
840K GLU* 3.1 28.5 - - + +
841K ALA 3.0 24.9 - - - +
842K GLU* 3.8 7.9 - - - -
843K PRO* 4.1 13.9 - - + -
871K TYR* 3.9 17.5 - - - +
910K MET* 4.9 10.3 - - + -
67L ARG* 3.2 5.8 + - - +
68L SER* 1.3 82.2 - - - +
70L VAL* 1.3 63.5 + - + +
72L THR* 2.2 25.5 + - - -
73L LEU* 2.9 31.0 + - + +
90L LEU* 6.0 3.8 - - + -
92L GLN* 5.9 0.9 - - - +
93L SER* 5.6 2.9 - - - +
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Residues in contact with VAL 70 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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722K ARG* 6.3 0.2 - - - +
812K TYR* 4.0 22.0 - - + -
814K LEU* 3.9 33.2 - - + -
834K ALA* 5.5 0.7 - - + -
836K VAL* 4.9 8.3 - - + -
843K PRO* 4.7 9.6 - - + -
871K TYR* 3.4 38.6 - - + +
69L ILE* 1.3 76.8 - - + +
71L ARG* 1.3 59.3 + - - +
73L LEU* 3.7 9.7 - - + +
74L HIS* 2.6 36.6 + - - +
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Residues in contact with ARG 71 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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722K ARG* 5.9 2.0 - - - +
787K GLU* 3.3 23.6 + - - +
812K TYR* 2.6 42.0 + - + -
836K VAL* 4.0 13.7 - - - +
67L ARG* 6.5 0.2 - - - -
68L SER* 3.3 34.4 - - - +
70L VAL* 1.3 81.9 - - - +
72L THR* 1.3 51.6 + - + +
74L HIS* 3.1 5.3 + - - +
75L GLN* 2.5 54.2 + - + +
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Residues in contact with THR 72 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67L ARG 4.3 2.6 + - - +
68L SER* 2.5 39.9 + - - +
69L ILE* 2.2 33.3 + - - -
71L ARG* 1.3 73.1 - - - +
73L LEU* 1.3 56.6 + - - +
75L GLN* 3.6 7.3 - - + +
76L HIS* 2.8 30.8 + - - +
81L ALA* 4.6 7.6 - - + +
85L SER* 5.6 10.1 - - - +
86L VAL* 4.5 18.5 - - - +
89L GLY* 6.4 2.0 - - - -
90L LEU* 5.9 1.7 - - - +
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Residues in contact with LEU 73 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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871K TYR* 4.6 1.1 - - + -
910K MET* 4.7 5.2 - - - -
912K LEU* 4.0 26.9 - - + -
913K TYR* 5.8 1.8 - - - +
926K LEU* 3.9 26.2 - - + -
1003K PHE* 5.7 0.2 - - - -
69L ILE* 2.9 38.7 + - + +
70L VAL* 3.7 19.7 - - + +
71L ARG 3.3 0.2 - - - -
72L THR* 1.3 75.9 + - - +
74L HIS* 1.3 57.9 + - - +
76L HIS* 3.4 8.7 + - - +
77L LYS* 3.0 28.6 + - + +
86L VAL* 5.2 7.2 - - + -
90L LEU* 4.6 12.8 - - + -
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Residues in contact with HIS 74 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360K VAL* 3.8 30.9 - - + +
720K SER* 5.7 1.4 - - - -
721K PRO 4.5 1.6 + - - -
722K ARG* 3.0 54.3 + - - +
70L VAL 2.6 22.8 + - - +
71L ARG* 3.6 5.2 - - - +
73L LEU* 1.3 71.9 - - - +
75L GLN* 1.3 55.1 + - - +
76L HIS 3.0 1.6 - - - -
77L LYS* 2.7 27.8 + - + +
78L LEU* 2.7 56.7 + - + +
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Residues in contact with GLN 75 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382K PHE* 4.4 7.1 - - - -
722K ARG* 6.1 0.8 - - - +
787K GLU* 5.8 1.0 + - - -
71L ARG* 2.5 43.1 + - + +
72L THR* 3.7 6.3 - - + +
74L HIS* 1.3 74.5 - - + +
76L HIS* 1.3 56.8 + - - +
78L LEU* 3.1 27.3 + - - +
79L GLY 3.0 3.6 + - - -
80L ARG* 2.7 77.7 + - + +
81L ALA* 3.2 20.6 + - + +
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Residues in contact with HIS 76 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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970K ASN* 3.6 29.1 + - + -
972K PHE* 5.5 3.6 - - - -
1003K PHE* 3.3 40.2 - + + -
1033K VAL* 3.9 3.3 - - - +
72L THR 2.8 13.5 + - - +
73L LEU* 3.5 12.3 - - - +
75L GLN* 1.3 73.9 - - - +
77L LYS* 1.3 63.3 + - - +
78L LEU 3.0 1.6 - - - -
79L GLY* 3.2 12.3 + - - +
81L ALA* 4.1 14.3 - - - +
83L TRP* 3.8 35.8 + + + +
86L VAL* 3.3 25.4 - - + +
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Residues in contact with LYS 77 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358K PRO* 3.9 7.8 - - - +
360K VAL* 2.9 30.6 + - + +
722K ARG 4.7 2.6 + - - -
723K LYS* 4.3 21.0 - - - +
913K TYR* 5.7 12.1 - - + +
955K SER 5.5 4.7 - - - +
1003K PHE* 4.0 11.2 - - + -
1005K ASN* 2.7 57.1 + - - +
1033K VAL* 3.4 10.7 - - - +
73L LEU 3.0 17.9 + - - +
74L HIS* 2.7 37.0 + - + +
76L HIS* 1.3 72.2 - - - +
78L LEU* 1.3 56.8 + - - +
79L GLY 3.5 0.2 - - - -
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Residues in contact with LEU 78 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327K ARG* 3.9 9.0 + - - -
328K LEU* 4.4 3.9 - - + +
358K PRO* 3.5 33.9 - - + +
360K VAL* 4.0 10.5 - - + -
380K GLY 4.4 5.8 - - - +
381K ALA* 4.6 12.3 - - + -
382K PHE* 5.3 2.7 - - + -
720K SER* 6.4 1.3 - - - -
1033K VAL* 3.3 15.0 - - - +
74L HIS* 2.7 40.1 + - + +
75L GLN* 3.1 38.6 - - - +
76L HIS 3.0 0.4 - - - -
77L LYS* 1.3 74.7 - - - +
79L GLY* 1.3 56.7 + - - +
80L ARG* 3.1 25.3 + - + +
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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