Contacts of the strand formed by residues 3 - 15 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1D MET 3.5 21.5 - - - -
3D PHE* 3.9 19.7 - + + -
1E MET* 3.0 54.0 + - - -
2E ASP* 1.3 76.4 - - - +
4E ARG* 1.3 70.5 - - - +
94E ARG* 3.5 30.1 - - + -
155E LEU* 4.0 22.0 - - + -
156E VAL 3.3 13.9 - - - -
157E VAL* 3.8 14.8 - - + -
3F PHE* 3.7 17.9 - + + -
94F ARG* 4.4 7.6 + - - +
155F LEU* 3.2 27.3 - - + +
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Residues in contact with ARG 4 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2E ASP* 2.8 40.5 + - - +
3E PHE* 1.3 86.7 - - - +
5E ILE* 1.3 59.3 + - - +
53E ALA* 3.2 28.0 + - - +
55E ALA* 5.3 1.4 - - - +
91E PHE* 3.8 29.9 - - + -
155E LEU* 3.5 8.9 - - - +
156E VAL* 2.9 37.4 + - + +
158E ARG* 4.0 18.0 - - - +
95F ASN* 3.3 25.6 - - - +
127F ASP* 3.2 30.5 + - - -
128F ARG* 3.4 27.6 - - - +
155F LEU* 4.1 1.6 - - - -
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Residues in contact with ILE 5 (chain E).
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* 3.5 26.5 - - + -
153D ALA* 6.2 0.9 - - + -
4E ARG* 1.3 72.1 - - - +
6E GLY* 1.3 66.1 + - - +
53E ALA* 3.5 8.3 - - - -
153E ALA* 5.8 1.3 - - + -
154E ALA 3.4 3.1 - - - -
155E LEU* 4.8 3.8 - - + +
5F ILE* 4.0 34.5 - - + -
6F GLY 5.0 1.8 - - - +
95F ASN* 2.9 41.3 + - - +
97F ASP* 3.7 5.4 - - - +
153F ALA* 4.0 27.6 - - + +
154F ALA 3.9 6.7 - - - +
155F LEU* 3.8 23.8 - - + +
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Residues in contact with GLY 6 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E ILE* 1.3 80.4 - - - +
7E GLN* 1.3 61.1 + - - +
49E ALA* 3.4 23.1 - - - -
53E ALA* 3.5 5.0 - - - +
153E ALA* 3.3 6.1 - - - +
154E ALA 2.9 32.1 + - - +
97F ASP* 3.4 10.3 - - - -
153F ALA* 4.9 0.7 - - - -
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Residues in contact with GLN 7 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E GLY* 1.3 74.8 - - - +
8E GLY* 1.3 62.4 + - - +
49E ALA* 3.6 8.8 - - - +
152E ALA 3.3 9.6 - - - +
153E ALA* 5.2 2.0 - - + -
97F ASP* 2.9 10.0 + - - +
98F SER* 3.2 14.5 - - - +
99F THR* 2.6 29.8 + - - +
132F LYS* 2.9 44.3 + - - +
151F GLN* 2.9 35.2 - - - +
152F ALA 4.5 1.6 - - - -
153F ALA* 4.0 30.3 - - + +
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Residues in contact with GLY 8 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E GLN* 1.3 80.7 - - - +
9E TYR* 1.3 60.6 + - - +
45E ALA* 3.4 22.7 - - - -
48E ASP* 4.1 6.1 - - - -
49E ALA* 3.7 5.6 - - - +
151E GLN* 3.4 5.4 - - - +
152E ALA 2.9 33.0 + - - +
99F THR* 5.0 0.2 - - - -
132F LYS* 4.7 1.3 - - - -
151F GLN* 4.8 0.7 - - - +
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Residues in contact with TYR 9 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E GLY* 1.3 73.9 - - - +
10E ASP* 1.3 67.0 + - - +
11E VAL* 3.6 23.2 - - + +
44E HIS 5.4 0.3 - - - +
45E ALA* 4.1 6.1 - - - +
48E ASP* 4.2 7.1 + - - +
141E TYR* 4.0 7.4 + - - -
149E GLU* 3.4 38.0 + - + -
150E ALA 3.5 6.3 - - - -
151E GLN* 4.7 5.4 - - + +
99F THR* 4.8 10.5 + - + +
101F ILE* 3.3 30.8 - - + +
134F LYS* 3.4 29.7 + - + +
135F THR 4.8 3.6 - - - -
136F ASN* 2.6 29.7 + - - -
142F LEU* 5.1 1.9 - - - +
149F GLU* 5.2 1.7 + - - -
151F GLN* 3.5 34.1 - - - +
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Residues in contact with ASP 10 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E TYR* 1.3 81.5 - - - +
11E VAL* 1.3 72.4 + - - +
12E HIS* 3.1 7.9 + - - -
41E VAL* 3.5 23.3 - - - +
44E HIS* 2.9 15.9 + - + +
45E ALA* 4.1 2.9 - - - +
149E GLU* 3.3 6.1 - - - +
150E ALA 2.9 32.1 + - - +
163E ZN 1.8 37.1 - - - -
134F LYS* 2.7 26.7 + - - +
137F GLU* 5.5 1.0 - - - +
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Residues in contact with VAL 11 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E TYR* 3.6 13.0 - - + +
10E ASP* 1.3 80.3 + - - +
12E HIS* 1.3 72.4 + - - +
41E VAL* 3.8 0.7 - - - -
141E TYR* 4.2 14.8 - - + +
142E LEU* 4.5 0.9 - - + -
148E ILE 3.4 22.2 - - - +
149E GLU* 4.2 7.0 - - + -
134F LYS* 5.2 0.2 - - - +
135F THR 4.7 2.2 - - - +
136F ASN* 3.4 47.6 - - - +
137F GLU* 3.2 17.5 - - - +
139F LEU* 3.6 21.1 - - + -
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Residues in contact with HIS 12 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10E ASP* 3.2 9.7 + - - -
11E VAL* 1.3 78.8 + - - +
13E GLN* 1.4 64.2 + - - +
33E LEU* 3.6 13.2 - - + +
34E LEU 2.9 23.1 + - - +
35E GLY* 4.3 7.6 - - - -
36E HIS 5.6 0.2 - - - -
39E ALA* 3.7 21.9 - - + +
41E VAL* 3.3 21.3 - - + +
44E HIS* 3.6 3.6 + + - -
147E GLY* 3.1 2.8 - - - -
148E ILE 3.0 30.5 + - - -
163E ZN 2.1 36.2 - - - -
137F GLU* 4.0 26.2 - - + -
139F LEU* 4.0 6.4 - - - +
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Residues in contact with GLN 13 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E HIS* 1.4 74.2 - - - +
14E LEU* 1.3 59.4 + - - +
15E VAL* 4.0 12.5 - - + +
33E LEU* 3.3 3.9 - - - -
34E LEU* 2.9 53.6 + - + +
146E GLU 3.4 9.0 - - - +
147E GLY* 4.0 0.4 - - - -
137F GLU* 2.9 33.3 + - + +
138F LYS* 3.9 18.2 + - - +
139F LEU* 3.9 18.5 - - + +
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Residues in contact with LEU 14 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13E GLN* 1.3 72.4 - - - +
15E VAL* 1.3 63.7 + - - +
20E LEU* 4.1 5.8 - - + -
29E TYR* 4.2 20.0 - - + +
31E ARG* 3.6 29.5 + - + +
32E GLY* 3.3 31.0 - - - +
33E LEU* 3.8 13.5 - - + -
104E ALA 4.5 5.6 - - - +
145E GLY* 3.5 30.2 - - - +
146E GLU* 3.0 9.1 + - - +
147E GLY* 3.8 13.0 - - - +
148E ILE* 4.0 25.4 - - + -
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Residues in contact with VAL 15 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13E GLN* 4.5 10.5 - - + +
14E LEU* 1.3 84.0 - - - +
16E PRO* 1.3 87.7 - - + +
17E GLY 3.7 0.2 + - - -
18E ARG* 4.1 4.2 + - + -
31E ARG* 3.6 7.9 - - - +
32E GLY* 2.9 28.6 + - - +
34E LEU* 3.9 44.6 - - + -
146E GLU 5.5 0.2 - - - +
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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