Contacts of the helix formed by residues 2 - 14 (chain F) in PDB entry 4UM3
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 ASP 2 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2B ASP* 3.7 16.1 - - - +
5B ASP* 4.5 8.8 - - - +
1F LEU* 1.3 74.8 - - - +
3F ARG* 1.3 65.6 + - - +
4F ALA* 3.5 11.7 + - - +
5F ASP* 2.9 31.0 + - - +
6F ILE* 3.1 27.8 + - - +
71F PRO* 4.4 4.7 - - - -
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Residues in contact with ARG 3 (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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2F ASP* 1.3 73.9 - - - +
4F ALA* 1.3 58.8 + - - +
6F ILE* 3.2 7.2 + - - +
7F LEU* 2.9 47.0 + - + +
71F PRO* 3.9 32.9 - - + +
73F GLN 4.6 7.9 + - - -
74F VAL* 4.0 16.5 - - + +
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Residues in contact with ALA 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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5B ASP* 4.6 15.0 - - - +
2F ASP* 3.2 13.7 + - - +
3F ARG* 1.3 79.4 - - - +
5F ASP* 1.3 59.0 + - - +
7F LEU* 3.9 6.5 - - - +
8F TYR* 3.0 29.7 + - - +
11F ARG* 5.3 1.0 + - - -
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Residues in contact with ASP 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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15A ARG* 5.3 4.2 + - - -
2B ASP* 4.6 7.2 - - - +
4B ALA* 4.6 15.2 - - - +
5B ASP* 5.2 3.3 - - - +
1F LEU* 3.7 24.3 - - + +
2F ASP* 2.9 31.7 + - - +
4F ALA* 1.3 78.4 - - - +
6F ILE* 1.3 59.5 + - - +
8F TYR* 3.2 8.3 + - - +
9F ASN* 2.8 38.3 + - - +
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Residues in contact with ILE 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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1F LEU* 4.3 17.7 - - + -
2F ASP 3.1 16.4 + - - +
3F ARG 3.6 5.8 - - - +
5F ASP* 1.3 74.1 - - - +
7F LEU* 1.3 60.1 + - - +
9F ASN* 3.3 9.2 + - - +
10F ILE* 3.0 38.7 + - + +
65F TRP* 3.4 65.5 - - + +
70F SER* 4.5 2.9 - - - -
71F PRO* 4.0 23.3 - - + -
74F VAL* 4.2 11.9 - - + -
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Residues in contact with LEU 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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3F ARG* 2.9 35.5 + - + +
4F ALA* 4.0 5.8 - - - +
6F ILE* 1.3 73.8 - - - +
8F TYR* 1.3 66.4 + - - +
10F ILE* 3.4 4.5 + - + +
11F ARG* 3.0 34.8 + - - +
74F VAL* 4.2 15.5 - - + -
75F SER 3.5 24.9 - - - +
76F VAL* 3.8 25.1 - - + -
77F PRO* 5.3 3.4 - - + -
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Residues in contact with TYR 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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12A GLN 3.4 22.3 + - - -
13A THR* 4.0 17.6 - - - -
14A SER 5.1 0.9 + - - -
15A ARG* 4.3 27.8 - - + -
8B TYR* 5.7 10.5 - + - -
11B ARG* 5.6 4.1 + - - -
4F ALA 3.0 19.4 + - - +
5F ASP* 3.2 8.3 + - - +
7F LEU* 1.3 77.0 - - - +
9F ASN* 1.3 74.3 + - - +
11F ARG* 3.4 29.5 + - - +
12F GLN* 3.0 50.1 + - + +
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Residues in contact with ASN 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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13A THR* 3.4 32.6 - - + +
1F LEU* 4.3 19.4 - - - +
5F ASP* 2.8 29.9 + - - +
6F ILE* 3.8 7.0 - - - +
8F TYR* 1.3 79.7 - - - +
10F ILE* 1.3 56.2 + - + +
13F THR* 2.5 43.9 + - - +
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Residues in contact with ILE 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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6F ILE* 3.0 38.6 + - + +
7F LEU* 3.7 6.3 - - + +
9F ASN* 1.3 76.7 - - + +
11F ARG* 1.3 60.7 + - - +
13F THR* 4.3 2.7 - - - -
14F SER* 2.8 39.0 + - - +
63F LEU* 4.2 20.2 - - + +
65F TRP* 4.6 2.5 - - + -
74F VAL* 4.2 5.8 - - + -
76F VAL* 3.9 43.1 - - + -
80F SER* 4.3 4.3 - - - +
81F LEU* 4.1 15.3 - - + -
105F VAL* 4.5 15.7 - - + -
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Residues in contact with ARG 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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8B TYR* 5.7 2.8 + - - -
4F ALA 5.3 0.8 + - - -
7F LEU* 3.0 19.2 + - - +
8F TYR* 3.8 39.3 - - - +
10F ILE* 1.3 80.5 - - + +
12F GLN* 1.3 74.0 + - - +
13F THR 3.6 0.2 + - - -
14F SER* 4.5 6.5 + - - +
80F SER* 4.2 23.5 - - - +
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Residues in contact with GLN 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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8A TYR* 3.6 20.6 + - - -
12A GLN* 2.8 64.5 + - + +
13A THR* 3.9 6.3 - - + -
8F TYR* 3.0 45.3 + - + +
9F ASN 3.8 2.9 - - - +
11F ARG* 1.3 93.8 + - + +
13F THR* 1.3 58.3 + - - +
14F SER 4.6 1.8 - - - +
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Residues in contact with THR 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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8A TYR* 4.3 6.8 - - + -
9A ASN* 3.2 44.4 - - + +
12A GLN* 4.2 4.7 - - + -
13A THR* 3.6 27.6 - - + -
9F ASN* 2.5 29.0 + - - +
10F ILE* 4.3 1.4 - - - -
12F GLN* 1.3 75.2 - - - +
14F SER* 1.3 67.5 + - - +
15F ARG* 3.5 13.2 + - - +
62F THR 5.4 3.6 + - - -
63F LEU* 5.8 1.2 - - - +
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Residues in contact with SER 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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8A TYR* 5.5 0.5 + - - -
10F ILE* 2.8 24.5 + - - +
11F ARG 4.5 6.6 + - - +
12F GLN 4.6 1.7 - - - +
13F THR* 1.3 77.6 + - - +
15F ARG* 1.3 63.3 + - - +
16F PRO* 3.3 10.4 - - - +
60F ASP* 6.0 0.4 - - - -
63F LEU* 3.8 28.2 - - - +
80F SER* 2.3 31.4 + - - -
81F LEU* 4.2 5.0 - - - -
82F TRP 5.6 0.7 - - - -
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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