Contacts of the strand formed by residues 64 - 71 (chain F) in PDB entry 3SHD
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 HIS 64 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63E GLN* 4.1 4.7 - - - -
64E HIS* 3.6 34.5 - + - -
85E ALA* 6.0 0.2 - - + -
87E GLU* 3.2 41.5 + - + +
135E ARG* 4.0 14.8 + - - -
63F GLN* 1.3 86.1 + - - +
65F PHE* 1.3 62.0 + - - +
84F PHE* 3.3 10.0 - - - +
85F ALA* 2.9 30.3 + - + +
135F ARG* 3.6 35.4 - - + -
136F TYR 3.5 17.5 - - - +
137F PRO* 5.2 2.2 - - + -
138F LEU* 3.8 6.7 - - - -
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Residues in contact with PHE 65 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64F HIS* 1.3 72.7 - - - +
66F ILE* 1.3 59.7 + - - +
67F ARG* 3.1 32.1 - - - -
68F MET* 3.5 12.6 - - + -
82F PHE* 3.8 23.3 - + + -
83F LEU 3.4 15.0 - - - -
84F PHE* 4.1 20.9 - + + -
135F ARG* 4.2 0.7 - - - -
136F TYR* 2.8 37.0 + - + +
137F PRO 3.8 16.8 - - - +
138F LEU* 4.0 5.3 - - - +
140F MET* 4.0 15.0 - - + -
141F ILE* 4.3 21.5 - - + -
65K PHE* 5.4 1.3 - + - -
140K MET* 3.1 40.4 - - + -
141K ILE* 5.4 2.0 - - + -
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Residues in contact with ILE 66 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11F VAL* 4.3 13.9 - - + -
65F PHE* 1.3 75.7 - - - +
67F ARG* 1.3 70.3 + - + +
83F LEU* 2.8 26.6 + - + +
84F PHE 3.5 13.9 - - - +
85F ALA* 3.5 35.4 - - + +
129F CYS* 3.6 39.0 - - + +
130F TYR* 4.3 14.6 - - + -
134F GLN 4.6 7.3 - - - +
135F ARG* 4.2 13.7 - - - +
136F TYR* 3.2 28.5 - - - -
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Residues in contact with ARG 67 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65F PHE* 3.1 19.4 - - - -
66F ILE* 1.3 91.5 - - + +
68F MET* 1.3 79.9 + - - +
69F HIS* 3.5 33.5 + - + -
83F LEU* 3.0 28.6 + - + +
125F GLU* 5.2 0.8 + - - -
129F CYS* 4.2 8.4 - - - -
64I HIS* 4.0 10.1 + - - -
139K GLU* 2.8 55.0 + - - +
140K MET* 3.5 13.9 - - + +
142K GLY* 3.1 40.2 + - - -
143K ASP 3.9 8.3 + - - -
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Residues in contact with MET 68 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65F PHE* 3.5 4.2 - - + -
67F ARG* 1.3 93.7 + - - +
69F HIS* 1.3 88.2 + - - +
70F GLN* 3.8 4.7 - - + +
80F LEU* 3.7 31.6 - - + -
81F ARG 3.2 20.0 - - - +
82F PHE* 3.7 39.5 - - + -
44K LEU* 4.1 7.9 - - + -
82K PHE* 3.8 11.0 - - - -
140K MET 3.0 15.1 + - - +
141K ILE* 3.6 31.6 - - + +
142K GLY 3.6 6.9 + - - +
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Residues in contact with HIS 69 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67F ARG* 3.5 41.8 + - + +
68F MET* 1.3 79.8 - - - +
70F GLN* 1.3 63.2 + - - +
71F TRP* 4.8 0.9 - - - +
79F PHE 3.6 1.2 - - - +
80F LEU* 3.5 3.8 - - - -
81F ARG* 2.9 42.8 + - + +
83F LEU* 4.6 16.2 - - + +
122F LEU* 3.6 39.6 - - + +
125F GLU* 3.6 20.2 + - + -
126F SER* 5.3 2.5 - - - -
129F CYS* 3.9 14.4 - - - -
142K GLY 3.4 3.6 - - - -
144K PHE* 3.9 19.3 - + + -
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Residues in contact with GLN 70 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2F PHE* 5.7 3.0 - - - -
68F MET* 3.8 9.4 - - + +
69F HIS* 1.3 72.2 - - - +
71F TRP* 1.3 62.7 + - - +
79F PHE 3.4 4.9 - - - +
80F LEU* 3.4 25.3 - - + +
38K LEU* 4.1 12.7 - - - +
42K GLU 3.1 22.4 + - - -
43K THR* 3.0 31.2 + - - +
44K LEU* 3.1 15.1 + - - +
141K ILE 4.5 1.3 - - - +
142K GLY 2.8 16.0 + - - +
143K ASP* 3.1 7.4 - - - +
144K PHE* 2.7 30.3 + - - +
146K TRP* 4.1 15.2 - - + -
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Residues in contact with TRP 71 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69F HIS 4.8 1.8 - - - +
70F GLN* 1.3 80.6 - - - +
72F ILE* 1.3 66.8 - - - +
73F ALA* 3.4 42.6 - - + +
74F PRO* 4.2 10.1 - - + -
78F PRO* 3.9 1.7 - - - +
79F PHE* 3.1 68.5 + + + +
81F ARG* 5.8 2.2 - - + -
120F SER* 3.7 30.7 - - - -
121F PRO* 4.2 10.5 - - + +
122F LEU* 3.7 29.1 - - + +
158F SO4 5.3 7.4 - - - -
144K PHE* 3.6 33.7 - + + +
145K ASN* 4.6 16.7 - - + +
146K TRP* 4.4 6.1 - - - -
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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