Contacts of the strand formed by residues 79 - 87 (chain A) in PDB entry 3F9C
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 THR 79 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A LEU 4.5 0.2 - - - -
71A MET* 3.1 8.5 - - - +
72A PHE 2.8 40.3 + - - -
78A GLY* 1.3 72.8 - - - -
80A PHE* 1.3 66.0 + - - +
81A LEU* 3.9 12.1 - - + -
177A VAL* 5.4 2.0 - - + -
180A ARG* 4.1 0.4 - - - -
228A GLU* 4.8 1.4 + - - +
231A GLN* 3.2 31.8 + - - +
232A ALA* 3.6 35.6 + - + -
235A LEU* 3.8 17.7 - - + +
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Residues in contact with PHE 80 (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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69A ASP* 4.5 0.9 - - + -
70A LEU 3.6 9.6 - - - -
71A MET* 3.6 29.8 - - + -
79A THR* 1.3 74.4 - - - +
81A LEU* 1.3 70.5 + - - +
157A ARG* 3.5 31.4 - - - -
177A VAL* 3.5 6.2 - - - +
178A GLU* 2.7 68.3 + - + +
180A ARG* 3.4 23.4 - - - +
187A THR* 3.7 12.1 - - - -
188A TYR* 3.7 32.3 - + - -
249A LEU* 3.9 18.6 - - + -
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Residues in contact with LEU 81 (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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69A ASP* 3.5 4.2 - - - +
70A LEU* 2.9 60.4 + - + +
79A THR* 3.9 20.0 - - + -
80A PHE* 1.3 78.3 - - - +
82A ARG* 1.3 63.3 + - - +
83A LEU* 3.7 33.4 - - + +
157A ARG* 3.9 7.5 - - - +
175A ALA* 3.9 6.7 - - + -
176A ALA 3.1 18.8 - - - +
177A VAL* 4.2 5.4 - - + -
232A ALA* 4.1 5.2 - - + +
235A LEU* 4.7 1.3 - - + -
236A ILE* 3.5 31.6 - - + -
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Residues in contact with ARG 82 (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* 3.5 23.1 - - - -
68A THR 3.6 0.9 - - - +
69A ASP* 2.9 42.3 + - - +
81A LEU* 1.3 74.6 - - - +
83A LEU* 1.3 61.0 + - - +
84A TYR* 3.6 25.8 + - + -
95A THR* 3.6 12.1 - - - +
96A LEU 3.3 21.8 + - - -
97A TRP* 4.0 2.2 + - - +
99A PRO* 4.0 13.7 - - - +
130A THR* 4.9 3.4 - - - +
134A TRP* 3.7 19.4 - - - -
157A ARG* 3.6 27.3 - - + +
158A THR* 3.6 28.3 + - - +
161A SER* 6.3 0.2 - - - -
174A VAL 3.5 1.0 - - - +
175A ALA* 3.7 0.3 - - - -
176A ALA* 2.8 35.9 + - + +
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Residues in contact with LEU 83 (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* 3.3 10.6 - - - -
68A THR* 2.8 49.9 + - + +
70A LEU* 5.4 2.0 - - + -
81A LEU* 3.7 22.3 - - + +
82A ARG* 1.3 73.2 - - - +
84A TYR* 1.3 60.0 + - - +
85A TYR* 3.9 14.8 - - + -
173A ILE* 3.6 22.0 - - + -
174A VAL 3.1 19.7 - - - +
175A ALA* 4.1 7.0 - - + -
236A ILE* 4.8 10.8 - - + -
253A PHE* 4.8 2.9 - - + -
255A MET* 4.8 4.3 - - + -
258A LEU* 3.7 37.9 - - + -
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Residues in contact with TYR 84 (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* 4.6 1.3 - - + -
66A GLY 3.4 6.5 - - - +
67A CYS* 3.8 28.0 - - + -
82A ARG* 3.6 22.6 + - + -
83A LEU* 1.3 72.5 - - - +
85A TYR* 1.3 63.8 + - - +
130A THR* 5.6 2.5 - - + -
132A ALA* 4.9 0.9 - - + -
157A ARG 3.9 10.0 + - - -
158A THR 3.9 3.6 + - - -
160A TYR 4.3 2.6 - - - -
161A SER* 3.5 39.3 + - - -
164A GLY* 3.8 35.7 - - - +
165A ILE* 4.0 18.2 - - + -
168A ALA* 3.9 7.2 - - + -
172A PHE 4.0 0.2 - - - +
173A ILE* 3.4 2.1 - - - +
174A VAL* 2.8 46.2 + - + +
176A ALA* 4.1 21.5 - - + -
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Residues in contact with TYR 85 (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* 3.4 5.0 - - - +
66A GLY* 2.8 42.6 + - - -
67A CYS* 3.3 28.7 + - - -
68A THR* 3.9 8.3 - - + -
83A LEU* 3.9 17.7 - - + -
84A TYR* 1.3 80.4 - - - +
86A PRO* 1.4 83.6 - - + +
87A SER* 4.3 0.4 - - - -
135A ASN* 3.6 3.3 - - - -
136A SER 2.6 42.6 + - - -
137A PRO 4.1 7.9 - - - -
138A LEU* 3.7 20.9 - - + -
168A ALA* 3.7 7.4 - - - +
172A PHE 3.9 2.2 - - - -
173A ILE* 4.0 11.7 - - + -
253A PHE* 3.3 25.1 - + - -
258A LEU* 5.9 0.7 - - + -
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Residues in contact with PRO 86 (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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63A TYR* 3.9 22.7 - - + -
64A SER 3.2 9.4 - - - +
85A TYR* 1.4 84.9 - - + +
87A SER* 1.3 60.3 + - - +
138A LEU* 3.4 10.5 - - + +
139A ARG* 3.1 28.2 + - + -
144A TYR* 3.8 22.9 - - + -
168A ALA 3.7 14.3 - - - +
171A GLY* 3.9 13.2 - - - -
172A PHE 3.2 18.8 - - - +
173A ILE* 4.2 7.2 - - + -
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Residues in contact with SER 87 (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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63A TYR* 5.6 0.2 - - - +
64A SER* 2.8 33.3 + - - +
65A VAL 3.5 7.4 + - - -
66A GLY* 3.8 9.9 - - - -
85A TYR* 3.2 2.9 + - - -
86A PRO* 1.3 75.8 - - - +
88A GLN* 1.3 68.7 + - - +
89A ASP 2.7 23.1 + - - -
133A ASN* 4.1 0.5 + - - -
136A SER* 3.6 18.6 + - - -
137A PRO 3.1 14.1 - - - -
139A ARG* 3.6 11.2 - - - +
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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