Contacts of the strand formed by residues 3 - 15 (chain F) in PDB entry 3F0D
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 PHE 3 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3D PHE* 3.7 26.2 - + + -
94D ARG* 4.4 7.3 + - - +
95D ASN* 4.4 0.2 - - - +
155D LEU* 3.1 28.9 - - + +
1E MET* 3.4 44.2 - - + -
3E PHE* 3.7 19.7 - + + -
1F MET* 3.1 13.3 + - - +
2F ASP* 1.3 78.6 - - - +
4F ARG* 1.3 70.9 + - - +
94F ARG* 3.7 28.0 - - + -
155F LEU* 3.9 24.9 - - + -
156F VAL 3.4 14.4 - - - +
157F VAL* 3.8 18.6 - - + -
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Residues in contact with ARG 4 (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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94D ARG 4.4 0.2 - - - -
95D ASN* 3.3 25.3 - - - +
127D ASP* 3.1 32.3 + - - -
128D ARG* 3.4 32.4 - - - +
155D LEU* 4.0 0.9 - - - -
2F ASP* 2.8 36.5 + - - +
3F PHE* 1.3 83.1 - - - +
5F ILE* 1.3 63.8 + - - +
53F ALA* 3.1 27.5 + - - +
55F ALA* 5.1 1.8 - - - +
91F PHE* 3.7 36.3 - - + -
154F ALA 3.9 0.2 - - - +
155F LEU* 3.5 4.5 - - - +
156F VAL* 3.0 37.3 + - + +
158F ARG* 4.3 9.7 - - - +
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Residues in contact with ILE 5 (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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5D ILE* 3.9 26.5 - - + -
6D GLY 4.6 1.6 - - - +
95D ASN* 2.8 42.1 + - - +
97D ASP* 3.8 5.9 - - - +
153D ALA* 4.0 15.3 - - + -
154D ALA* 3.3 38.8 - - - +
155D LEU* 3.9 11.9 - - + +
5E ILE* 4.0 22.7 - - + -
4F ARG* 1.3 77.0 - - - +
6F GLY* 1.3 59.9 + - - +
53F ALA* 3.4 9.9 - - - -
154F ALA 3.4 5.6 - - - +
155F LEU* 3.8 18.2 - - + -
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Residues in contact with GLY 6 (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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97D ASP* 3.4 9.9 - - - -
153D ALA* 4.9 4.1 - - - +
5E ILE* 5.0 1.6 - - - +
5F ILE* 1.3 78.7 - - - +
7F GLN* 1.3 61.3 + - - +
49F ALA* 3.4 23.8 - - - -
53F ALA* 3.6 3.9 - - - +
153F ALA* 3.4 5.7 - - - +
154F ALA 2.9 29.5 + - - +
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Residues in contact with GLN 7 (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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97D ASP* 2.9 11.5 + - - +
98D SER* 3.2 16.6 - - - +
99D THR* 2.7 28.2 + - - +
132D LYS* 2.8 43.6 + - - +
151D GLN* 3.0 32.9 + - - +
152D ALA 4.4 2.0 - - - -
153D ALA* 3.9 32.3 - - + +
6F GLY* 1.3 75.4 - - - +
8F GLY* 1.3 63.5 + - - +
49F ALA* 3.7 6.5 - - - +
152F ALA 3.4 9.0 - - - +
153F ALA* 5.3 1.6 - - + -
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Residues in contact with GLY 8 (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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132D LYS* 4.6 1.3 - - - -
151D GLN* 4.9 0.7 - - - +
7F GLN* 1.3 81.3 - - - +
9F TYR* 1.3 60.4 - - - +
45F ALA* 3.5 23.1 - - - -
48F ASP* 4.2 6.3 - - - -
49F ALA* 3.6 6.0 - - - +
151F GLN* 3.4 5.5 - - - +
152F ALA 2.9 32.2 + - - +
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Residues in contact with TYR 9 (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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99D THR* 4.9 6.5 + - + -
101D ILE* 4.2 17.5 - - + -
132D LYS* 5.7 0.2 - - - +
134D LYS* 3.1 40.2 + - + +
135D THR 4.9 1.1 - - - -
136D ASN* 2.5 34.6 + - - -
142D LEU* 5.2 1.7 - - + +
149D GLU* 5.4 4.0 + - - -
151D GLN* 3.5 36.8 - - - +
7F GLN* 4.7 0.9 + - - +
8F GLY* 1.3 74.3 - - - +
10F ASP* 1.3 65.9 + - - +
11F VAL* 3.7 19.2 - - + +
45F ALA* 4.3 4.9 - - - +
48F ASP* 4.3 6.8 - - - +
141F TYR* 3.8 10.7 + - - -
149F GLU* 3.4 38.4 + - + -
150F ALA 3.5 5.6 - - - -
151F GLN* 4.9 4.9 - - + -
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Residues in contact with ASP 10 (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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134D LYS* 3.1 21.5 + - - +
137D GLU* 5.5 1.0 - - - +
9F TYR* 1.3 82.4 - - - +
11F VAL* 1.3 71.9 + - - +
12F HIS* 2.9 9.7 + - - -
41F VAL* 3.5 20.4 - - + +
44F HIS* 3.0 12.3 + - + +
45F ALA* 4.1 8.3 - - + +
149F GLU* 3.3 5.9 - - - +
150F ALA 2.9 31.2 + - - +
163F ZN 1.9 38.4 - - - -
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Residues in contact with VAL 11 (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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134D LYS* 5.0 1.0 - - - +
135D THR 4.8 1.8 - - - +
136D ASN* 3.4 48.0 - - - +
137D GLU* 3.2 17.8 - - + +
139D LEU* 3.6 21.3 - - + -
9F TYR* 3.7 11.7 - - + +
10F ASP* 1.3 81.2 + - - +
12F HIS* 1.3 72.4 + - - +
41F VAL* 3.8 0.7 - - - -
141F TYR* 4.1 15.5 - - + -
148F ILE 3.4 22.9 - - - +
149F GLU* 4.2 6.3 - - + -
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Residues in contact with HIS 12 (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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137D GLU* 4.3 21.6 - - + -
139D LEU* 4.1 5.7 - - - +
10F ASP* 3.3 9.4 - - - -
11F VAL* 1.3 81.7 + - - +
13F GLN* 1.3 60.6 - - - +
33F LEU* 3.6 20.6 - - + +
34F LEU 2.9 25.0 + - - +
35F GLY* 4.4 7.0 - - - -
36F HIS 5.7 0.2 - - - -
39F ALA* 3.7 25.6 - - + -
41F VAL* 3.9 6.7 - - + -
44F HIS* 3.4 5.6 + + - -
147F GLY* 3.1 2.9 - - - -
148F ILE 3.0 30.7 + - - +
163F ZN 2.0 37.6 - - - -
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Residues in contact with GLN 13 (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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137D GLU* 3.7 28.3 - - + +
138D LYS* 4.5 17.2 + - - +
139D LEU* 3.8 24.8 - - + +
12F HIS* 1.3 73.0 - - - +
14F LEU* 1.3 61.5 + - - +
15F VAL* 4.3 14.5 - - + +
33F LEU* 3.4 4.9 - - - -
34F LEU* 2.9 51.2 + - + +
146F GLU* 3.4 8.9 + - - +
147F GLY* 4.1 0.7 - - - -
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Residues in contact with LEU 14 (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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12F HIS 3.8 0.2 + - - -
13F GLN* 1.3 72.8 - - - +
15F VAL* 1.3 63.1 + - - +
16F PRO* 4.9 0.3 - - - +
20F LEU* 4.0 14.4 - - + -
29F TYR* 4.4 10.8 - - + -
31F ARG* 3.5 41.2 + - + +
32F GLY* 3.4 19.7 - - - +
33F LEU* 3.7 23.3 - - + -
104F ALA 4.7 4.9 - - - +
145F GLY* 3.5 20.4 - - - +
146F GLU* 3.0 13.9 + - - +
147F GLY* 4.2 7.6 - - - +
148F ILE* 3.8 23.6 - - + -
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Residues in contact with VAL 15 (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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13F GLN* 4.2 9.2 - - + +
14F LEU* 1.3 79.0 - - - +
16F PRO* 1.3 82.7 - - + +
18F ARG* 3.7 22.0 + - + +
31F ARG* 3.3 7.5 - - - +
32F GLY 2.8 37.7 + - - +
34F LEU* 3.9 41.7 - - + -
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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