Contacts of the helix formed by residues 76 - 86 (chain L) in PDB entry 6XAV
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 76 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38L LEU* 4.3 19.4 - - + +
74L VAL* 4.5 2.5 - - + +
75L MET* 1.3 83.2 + - - +
77L ASP* 1.3 64.1 + - - +
78L ALA* 2.9 32.0 + - - +
79L SER* 2.7 28.6 + - - +
80L TRP* 2.8 14.2 + - - +
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Residues in contact with ASP 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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377I THR* 3.3 28.0 - - - +
378I ARG 4.7 1.0 + - - -
379I GLU* 2.9 37.2 - - + +
76L ASN* 1.3 79.4 + - - +
78L ALA* 1.3 62.6 + - - +
80L TRP* 3.3 17.1 + - - +
81L HIS* 3.4 17.2 - - - -
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Residues in contact with ALA 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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379I GLU* 5.4 5.1 - - + +
38L LEU* 6.2 2.5 - - + -
76L ASN* 2.9 13.2 + - - +
77L ASP* 1.3 77.7 - - - +
79L SER* 1.3 62.8 + - - +
81L HIS* 3.4 8.8 + - - +
82L LEU* 3.2 19.3 + - - +
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Residues in contact with SER 79 (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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38L LEU* 4.9 8.4 - - - +
39L PHE* 4.2 14.2 - - - -
73L MET* 3.9 20.1 - - - +
74L VAL 3.3 8.6 + - - -
75L MET* 3.9 1.9 - - - +
76L ASN* 2.7 41.4 + - - +
78L ALA* 1.3 76.0 - - - +
80L TRP* 1.3 58.8 + - - +
81L HIS 3.3 0.2 - - - -
82L LEU* 3.7 9.7 - - - +
83L VAL* 2.9 32.1 + - - +
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Residues in contact with TRP 80 (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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367I TYR* 3.6 15.0 - - - -
374I GLU* 3.3 28.5 - - - -
375I PRO* 4.2 16.2 - - + -
377I THR* 4.8 4.9 - - + -
75L MET* 3.7 20.0 - - + -
76L ASN 2.8 13.8 + - - +
77L ASP* 3.5 17.7 - - - +
78L ALA 3.2 0.4 - - - -
79L SER* 1.3 77.4 + - - +
81L HIS* 1.3 103.7 + + - +
83L VAL* 3.2 18.9 - - + +
84L ARG* 3.3 39.9 - - + +
92L PHE* 4.6 17.9 - + - +
97L SER* 4.0 16.3 + - - -
98L ASP 5.3 1.5 + - - -
100L PRO* 5.0 10.1 - - + +
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Residues in contact with HIS 81 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367I TYR* 4.2 5.4 - + - -
377I THR* 4.2 0.4 + - - -
379I GLU* 2.8 37.1 + - - +
380I ALA* 3.4 22.9 - - + +
77L ASP 3.4 17.5 - - - -
78L ALA* 3.4 8.5 + - - +
79L SER 3.3 0.2 - - - -
80L TRP* 1.3 107.9 - + - +
82L LEU* 1.3 52.9 + - - +
84L ARG* 3.1 9.6 + - - +
85L SER* 2.5 45.5 + - - +
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Residues in contact with LEU 82 (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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29L HIS* 5.0 12.8 - - + +
30L ILE* 5.5 6.7 - - + -
33L HIS* 3.5 52.9 - - + +
39L PHE* 3.6 32.8 - - + -
78L ALA 3.2 14.1 + - - +
79L SER* 3.2 9.6 + - - +
81L HIS* 1.3 79.7 - - - +
83L VAL* 1.3 62.5 + - - +
85L SER* 3.1 20.2 + - - -
86L VAL* 3.6 10.9 + - - +
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Residues in contact with VAL 83 (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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12L VAL* 3.6 24.8 - - + +
26L LEU* 5.0 9.2 - - + -
39L PHE* 5.5 7.4 - - + -
71L VAL* 5.9 0.4 - - + -
73L MET* 5.3 4.7 - - + -
79L SER 2.9 15.3 + - - +
80L TRP* 3.2 19.3 - - + +
82L LEU* 1.3 75.7 - - - +
84L ARG* 1.3 63.2 + - + +
85L SER 3.5 0.2 - - - -
86L VAL* 3.2 19.9 - - - +
89L VAL* 3.8 7.4 - - - +
91L GLY* 5.0 3.8 - - - -
92L PHE* 3.6 52.5 - - + +
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Residues in contact with ARG 84 (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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371I ARG* 4.6 16.6 - - - +
374I GLU* 5.5 6.1 + - - -
80L TRP* 3.3 52.8 + - - +
81L HIS* 3.1 11.5 + - - +
83L VAL* 1.3 86.1 - - + +
85L SER* 1.3 59.8 + - - +
86L VAL 3.4 6.9 - - - +
89L VAL* 4.6 8.0 - - - +
90L MET 3.4 23.5 + - - +
91L GLY* 4.5 14.3 - - - -
92L PHE 5.3 3.1 + - - +
97L SER* 6.4 0.2 - - - -
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Residues in contact with SER 85 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477I GLU* 4.6 4.7 - - - +
29L HIS* 5.3 4.5 + - - -
81L HIS* 2.5 31.6 + - - +
82L LEU* 3.1 16.1 + - - -
84L ARG* 1.3 73.3 - - - +
86L VAL* 1.3 63.8 + - - +
87L PRO* 3.4 7.3 - - - +
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Residues in contact with VAL 86 (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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12L VAL* 5.5 1.3 - - + -
22L VAL* 4.3 24.7 - - + +
25L SER* 4.4 14.8 - - - -
26L LEU* 4.9 16.6 - - + +
29L HIS* 4.7 14.6 - - + -
82L LEU 3.6 6.1 + - - +
83L VAL* 3.2 27.8 - - + +
84L ARG 3.9 3.3 - - - +
85L SER* 1.3 77.0 - - - +
87L PRO* 1.3 84.8 - - + +
88L ARG 3.8 0.2 + - - -
89L VAL* 3.2 23.8 - - + +
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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