Contacts of the strand formed by residues 75 - 82 (chain H) in PDB entry 6IY6
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 GLN 75 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71H ALA* 3.6 2.5 - - - +
72H LYS* 3.1 33.8 + - + +
73H GLY 4.1 2.3 - - - +
74H LYS* 1.3 85.4 - - + +
76H CYS* 1.3 58.3 - - - +
77H PHE* 3.6 33.0 - - + -
90H LEU* 4.4 18.4 - - + +
91H VAL 3.9 3.8 - - - -
92H ALA* 4.7 13.8 - - + +
102H VAL* 4.1 2.6 - - - +
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Residues in contact with CYS 76 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69H SER* 4.8 1.8 - - - -
70H ARG 3.8 5.4 - - - -
71H ALA* 3.9 10.3 - - + -
75H GLN* 1.3 73.3 - - - +
77H PHE* 1.3 67.7 + - - +
78H LEU* 3.7 13.5 - - - +
90H LEU* 3.6 2.3 - - - +
91H VAL 2.9 39.0 + - - +
102H VAL* 3.8 21.1 - - + +
105H ALA* 3.9 14.6 - - + -
106H ALA* 3.7 35.4 - - - -
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Residues in contact with PHE 77 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68H THR 4.3 0.2 - - - +
69H SER* 3.4 3.8 - - - -
70H ARG* 2.8 43.4 + - + +
71H ALA* 6.2 0.4 - - - -
75H GLN* 3.6 29.8 - - + -
76H CYS* 1.3 73.3 - - - +
78H LEU* 1.3 62.3 + - - +
88H GLN* 3.2 41.1 - - + -
89H ALA 3.4 4.5 - - - +
90H LEU* 3.4 39.0 - - + -
136H GLU* 4.1 0.9 - - - -
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Residues in contact with LEU 78 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66H VAL* 4.0 26.0 - - + -
68H THR 3.5 7.6 - - - +
69H SER* 4.2 6.1 - - - -
76H CYS* 3.7 13.0 - - - +
77H PHE* 1.3 79.9 - - - +
79H VAL* 1.3 60.9 + - - +
80H LEU* 3.8 12.1 - - + -
88H GLN* 3.6 7.1 - - - +
89H ALA* 2.8 50.1 + - + +
91H VAL* 3.6 31.2 - - + -
105H ALA* 3.9 19.5 - - + +
108H ILE* 4.9 0.2 - - + -
139H VAL* 5.1 0.4 - - + -
142H ILE* 3.9 22.4 - - + -
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Residues in contact with VAL 79 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65H ARG 3.6 0.2 - - - +
66H VAL* 3.8 0.6 - - - +
67H HIS* 2.8 52.4 + - + +
68H THR* 2.8 40.5 + - + +
78H LEU* 1.3 73.8 - - - +
80H LEU* 1.3 56.6 + - - +
86H ASN* 3.7 30.3 - - + +
87H VAL 3.5 6.5 - - - +
88H GLN* 5.5 3.8 - - + -
130H CYS* 4.3 12.8 - - - -
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Residues in contact with LEU 80 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48H VAL* 4.4 3.3 - - - +
62H VAL* 4.8 8.1 - - + -
64H ALA* 3.8 13.7 - - + -
65H ARG 3.3 8.1 - - - +
66H VAL* 4.6 6.7 - - + -
78H LEU* 4.3 17.5 - - + -
79H VAL* 1.3 68.1 - - - +
81H ARG* 1.3 59.0 + - - +
86H ASN* 3.2 1.8 - - - -
87H VAL* 2.9 47.6 + - + +
89H ALA* 3.5 28.5 - - + -
114H VAL* 4.0 25.8 - - + -
116H VAL* 3.9 20.4 - - + -
137H LEU* 3.8 22.0 - - + -
142H ILE* 5.6 0.4 - - + -
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Residues in contact with ARG 81 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261G ASP* 3.6 16.3 + - - -
48H VAL* 4.8 0.2 - - - -
64H ALA* 3.3 5.5 - - - +
65H ARG* 2.9 59.7 + - - +
67H HIS* 3.3 46.5 + - + -
79H VAL 3.4 0.4 + - - -
80H LEU* 1.3 73.5 - - - +
82H GLN* 1.3 66.8 + - - +
84H GLN* 4.7 9.2 - - - +
85H PHE 3.3 17.0 - - - +
86H ASN* 4.0 13.2 - - + +
111H GLU* 2.7 39.1 + - - -
188H ARG* 4.2 21.8 + - - +
189H THR* 5.9 0.6 - - - +
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Residues in contact with GLN 82 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261G ASP* 5.6 1.3 - - - -
263G GLU* 3.0 28.3 + - - +
46H VAL 4.7 1.5 + - - +
47H ARG* 3.5 23.2 - - - +
48H VAL* 2.7 47.4 + - + +
62H VAL* 6.0 0.2 - - - -
63H ARG 4.2 16.0 + - - +
64H ALA* 4.6 4.0 - - + -
65H ARG* 6.1 1.1 - - - +
81H ARG* 1.3 77.4 - - - +
83H GLN* 1.3 78.3 + - + +
84H GLN 3.5 1.3 - - - -
85H PHE* 2.7 25.9 + - - +
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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