Contacts of the helix formed by residues 7 - 18 (chain A) in PDB entry 1U1T
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 LEU 7 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A SER* 1.3 78.1 - - - +
8A GLN* 1.3 68.0 + - - +
9A ASP 3.4 1.8 - - - -
10A PRO* 3.1 7.7 - - - +
11A TYR* 3.0 27.4 + - - +
71A PRO* 3.7 24.4 - - + +
38F SER* 3.1 32.3 - - - +
39F PHE* 3.2 36.1 - - - +
40F ASP* 2.8 16.0 + - + +
43F VAL* 4.4 7.4 - - + -
45F LEU* 4.3 16.4 - - + -
53F MET* 5.3 0.2 - - - -
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Residues in contact with GLN 8 (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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6A SER* 4.6 4.0 - - - +
7A LEU* 1.3 80.0 - - - +
9A ASP* 1.3 62.0 + - - +
11A TYR* 3.4 0.7 - - - +
12A LEU* 2.8 47.2 + - + +
56A LYS* 2.8 29.4 + - - +
40F ASP* 3.4 9.3 + - - +
42F PHE* 4.1 26.1 - - - +
43F VAL* 4.2 5.4 - - + +
53F MET* 3.8 20.9 - - + -
55F TYR* 2.5 39.6 + - - +
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Residues in contact with ASP 9 (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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6A SER* 2.8 19.0 + - - -
8A GLN* 1.3 74.6 + - - +
10A PRO* 1.3 69.0 - - + +
12A LEU* 3.1 2.6 + - - +
13A ASN* 2.7 32.2 + - - +
39A PHE* 3.8 22.3 - - + -
40A ASP 5.5 1.4 - - - +
41A GLN* 6.1 0.7 - - - -
56A LYS* 4.8 9.5 + - - -
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Residues in contact with PRO 10 (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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6A SER* 3.6 20.6 - - - +
7A LEU 3.1 15.7 - - - +
9A ASP* 1.3 94.0 - - + +
11A TYR* 1.3 59.1 + - - +
13A ASN* 3.6 7.8 - - + +
14A THR* 2.9 29.6 + - - +
71A PRO* 3.3 26.5 - - + -
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Residues in contact with TYR 11 (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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7A LEU* 3.0 21.9 + - + +
8A GLN* 3.4 4.0 - - - +
10A PRO* 1.3 77.8 - - - +
12A LEU* 1.3 64.1 + - + +
14A THR* 3.3 5.9 + - - -
15A LEU* 3.2 44.8 + - + +
62A VAL* 3.9 10.2 + - + -
64A PRO* 3.0 24.1 - - + +
68A VAL* 4.3 11.0 - - + -
69A ARG 5.4 0.9 - - - -
70A LEU* 3.8 24.0 - - + -
71A PRO* 3.3 24.4 - - + +
45F LEU* 4.4 13.0 - - + -
51F SER 2.8 24.2 + - - -
53F MET* 3.6 39.5 + - + -
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Residues in contact with LEU 12 (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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8A GLN* 2.8 49.4 + - + +
9A ASP* 3.7 1.6 - - - +
11A TYR* 1.3 75.9 - - + +
13A ASN* 1.3 58.3 + - - +
15A LEU* 3.3 14.6 + - + +
16A ARG* 2.9 28.1 + - - +
36A ILE* 3.5 27.6 - - + +
39A PHE* 3.7 28.0 - - + -
44A ILE* 4.2 15.9 - - + -
56A LYS* 4.1 17.3 - - - +
62A VAL* 4.7 4.7 - - + -
53F MET* 4.3 14.8 - - + -
55F TYR* 4.2 3.4 - - - +
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Residues in contact with ASN 13 (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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9A ASP 2.7 22.1 + - - +
10A PRO* 3.6 9.2 - - + +
12A LEU* 1.3 73.1 - - - +
14A THR* 1.3 51.6 + - - +
16A ARG* 3.0 33.9 + - - +
17A LYS* 2.7 48.5 + - - +
39A PHE* 3.8 14.9 - - + -
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Residues in contact with THR 14 (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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10A PRO* 2.9 20.3 + - - +
11A TYR* 3.6 6.3 - - - -
13A ASN* 1.3 75.3 - - - +
15A LEU* 1.3 60.6 + - - +
17A LYS* 3.2 23.9 + - - +
18A GLU* 2.9 63.7 + - + +
20A VAL* 5.6 0.2 - - + -
68A VAL* 4.4 17.3 - - + -
69A ARG* 4.1 25.5 + - + +
71A PRO* 5.5 1.0 - - - +
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Residues in contact with LEU 15 (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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11A TYR* 3.2 40.4 + - + +
12A LEU* 3.6 8.1 - - + +
14A THR* 1.3 77.0 - - - +
16A ARG* 1.3 59.4 + - - +
19A ARG* 3.3 2.1 + - - -
20A VAL* 2.9 49.8 + - + +
22A VAL* 4.1 13.9 - - + -
36A ILE* 4.1 22.3 + - + +
62A VAL* 4.0 18.4 - - + -
64A PRO* 4.0 24.7 - - + -
68A VAL* 4.1 18.8 - - + -
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Residues in contact with ARG 16 (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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12A LEU 2.9 14.5 + - - +
13A ASN* 3.0 40.5 + - - +
14A THR 3.0 0.2 - - - -
15A LEU* 1.3 74.2 - - - +
17A LYS* 1.3 76.3 + - - +
18A GLU 3.1 1.1 - - - -
19A ARG* 2.8 30.5 + - - +
36A ILE* 3.5 31.1 - - + +
37A GLU* 3.2 24.1 + - - +
38A SER* 4.0 10.5 - - - +
39A PHE* 4.3 8.6 - - + -
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Residues in contact with LYS 17 (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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13A ASN* 2.7 28.4 + - - +
14A THR* 3.2 33.2 + - - +
16A ARG* 1.3 91.7 - - - +
18A GLU* 1.3 83.1 + - + +
19A ARG* 3.6 10.4 + - - +
69A ARG* 5.9 5.9 - - - +
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Residues in contact with GLU 18 (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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14A THR* 2.9 40.6 + - - +
17A LYS* 1.3 95.5 + - + +
19A ARG* 1.3 70.9 + - - +
20A VAL* 3.1 15.0 + - + +
66A ARG* 3.1 25.2 + - - +
68A VAL* 5.4 2.6 - - - +
69A ARG* 5.1 7.5 + - - +
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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