Contacts of the strand formed by residues 64 - 72 (chain A) in PDB entry 3F98
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 64 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58A ARG* 4.1 8.1 + - - +
62A PRO 4.0 1.8 + - - -
63A TYR* 1.3 76.2 - - - +
65A VAL* 1.3 59.7 + - - +
86A PRO* 3.5 6.2 - - - +
87A SER* 2.8 32.7 + - - -
88A GLN 4.5 2.5 + - - -
89A ASP 3.3 24.9 - - - -
90A ASN* 2.7 43.0 + - - +
133A ASN* 4.1 2.2 - - - -
524A FMT 5.4 1.4 + - - -
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Residues in contact with VAL 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A ARG* 5.3 2.4 - - - +
63A TYR 3.8 0.4 - - - +
64A SER* 1.3 81.1 - - - +
66A GLY* 1.3 67.3 + - - +
84A TYR* 4.2 6.7 - - + -
85A TYR 3.3 3.8 - - - +
87A SER* 3.4 4.5 - - - -
131A PRO 4.6 4.8 + - - +
132A ALA* 3.3 14.1 - - + -
133A ASN* 2.7 35.1 + - - +
165A ILE* 3.5 28.5 - - + +
168A ALA* 3.6 20.2 - - + -
169A SER* 3.4 37.9 - - - +
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Residues in contact with GLY 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A VAL* 1.3 79.5 - - - +
67A CYS* 1.3 61.0 + - - +
84A TYR* 3.3 5.7 - - - -
85A TYR* 2.8 52.9 + - - -
87A SER* 3.5 9.5 + - - -
132A ALA* 4.2 0.4 - - - -
133A ASN* 3.2 12.6 - - - -
136A SER* 4.4 0.7 - - - -
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Residues in contact with CYS 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A GLY* 1.3 75.5 - - - +
68A THR* 1.3 61.4 + - - +
82A ARG* 3.5 40.2 - - - -
83A LEU 3.2 8.7 - - - +
84A TYR* 3.9 10.8 - - + -
85A TYR* 3.4 6.4 + - - -
95A THR* 3.5 33.4 - - - +
132A ALA* 3.7 9.9 - - + -
133A ASN 3.1 6.3 + - - -
134A TRP* 3.2 9.2 - - - -
135A ASN 2.8 30.0 + - - -
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Residues in contact with THR 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A CYS* 1.3 73.6 - - - +
69A ASP* 1.3 74.6 + - - +
82A ARG* 3.5 2.1 - - - +
83A LEU* 2.8 47.4 + - + +
85A TYR* 3.9 7.6 - - + -
134A TRP* 3.7 10.1 - - - -
135A ASN* 2.7 26.8 + - - -
251A LEU* 3.8 6.2 - - - +
253A PHE* 3.6 34.0 - - + +
255A MET* 3.9 13.8 - - + +
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Residues in contact with ASP 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A THR* 1.3 82.8 + - - +
70A LEU* 1.3 63.4 + - - +
80A PHE* 4.4 1.6 - - + -
81A LEU* 3.5 3.1 - - - +
82A ARG* 2.9 44.8 + - - +
99A PRO* 5.1 0.3 - - - +
134A TRP* 3.5 8.4 - - - -
157A ARG* 2.8 36.2 + - - -
247A ASN* 3.0 17.7 + - - -
249A LEU* 3.6 21.2 - - + +
251A LEU* 3.4 17.7 - - + +
255A MET* 4.0 1.2 - - - +
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Residues in contact with LEU 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A THR* 5.7 0.7 - - + -
69A ASP* 1.3 75.9 - - - +
71A MET* 1.3 66.2 + - - +
72A PHE* 4.6 0.9 - - + -
79A THR* 3.7 1.0 - - - +
80A PHE* 3.4 4.7 - - - -
81A LEU* 2.9 60.0 + - + +
83A LEU* 5.9 2.0 - - + -
235A LEU* 3.8 22.9 - - + -
236A ILE* 5.5 3.8 - - + -
239A ILE* 3.7 23.8 - - + -
245A VAL* 4.4 14.6 - - + -
247A ASN* 3.6 27.4 - - + +
249A LEU* 4.6 0.4 - - - -
255A MET* 3.9 26.9 - - + -
258A LEU* 6.0 0.9 - - + -
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Residues in contact with MET 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A LEU* 1.3 74.1 - - - +
72A PHE* 1.3 64.1 + - - +
73A ASP 3.5 13.2 - - - +
74A HIS* 4.2 11.0 - - - +
79A THR 3.2 9.4 - - - +
80A PHE* 3.8 21.1 - - + -
180A ARG* 3.6 27.8 - - - +
188A TYR* 3.6 36.3 - - + +
189A TYR* 4.5 1.1 - - - -
190A PHE* 3.8 26.2 - - - -
247A ASN* 2.9 9.3 + - - +
248A ALA* 2.8 35.1 + - + +
249A LEU* 4.0 17.6 - - + +
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Residues in contact with PHE 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A LEU* 4.2 2.9 - - + -
71A MET* 1.3 73.5 - - - +
73A ASP* 1.3 75.0 + - + +
79A THR* 2.8 31.4 + - - -
235A LEU* 3.9 20.9 - - + +
243A LYS* 5.8 7.2 - - - -
244A PRO 5.7 1.6 - - - -
245A VAL* 3.7 34.8 - - + -
246A LYS* 3.2 36.1 - - + +
248A ALA* 5.3 0.7 - - + -
509A FMT 2.8 29.2 - - - +
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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