Contacts of the helix formed by residues 7 - 18 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A SER* 3.5 28.3 - - - +
39A PHE* 3.5 33.7 - - - +
40A ASP* 3.0 13.8 + - + +
43A VAL* 3.8 17.9 - - + +
45A LEU* 4.3 16.4 - - + -
53A MET* 5.8 1.6 - - + -
6B SER* 1.3 82.3 + - - +
8B GLN* 1.3 65.1 + - - +
9B ASP 3.4 1.1 - - - -
10B PRO* 3.4 3.3 - - - +
11B TYR* 3.2 30.7 + - + +
70B LEU* 3.9 20.9 - - + -
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Residues in contact with GLN 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A ASP* 2.9 13.7 + - - +
42A PHE* 4.1 22.0 - - - +
43A VAL* 4.2 8.3 - - + +
53A MET* 4.1 20.2 - - - -
55A TYR* 2.7 33.6 + - - +
5B HIS* 3.6 26.9 + - - +
7B LEU* 1.3 79.0 - - - +
9B ASP* 1.3 58.0 + - - +
11B TYR* 3.4 1.2 + - - +
12B LEU* 2.9 46.1 + - + +
56B LYS* 2.8 25.3 + - - +
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Residues in contact with ASP 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B HIS* 2.9 50.6 + - - +
8B GLN* 1.3 74.1 - - - +
10B PRO* 1.3 69.3 - - + +
12B LEU 3.4 0.3 + - - -
13B ASN* 2.8 34.4 + - - +
39B PHE* 3.9 20.3 - - + -
56B LYS* 5.5 1.2 + - - -
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Residues in contact with PRO 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B HIS 4.1 0.2 - - - +
6B SER* 3.3 26.5 - - - +
7B LEU 3.4 9.4 - - - +
9B ASP* 1.3 95.0 - - + +
11B TYR* 1.3 54.1 + - - +
13B ASN* 3.8 5.5 - - + +
14B THR* 2.7 39.7 + - - +
70B LEU* 4.1 20.4 - - + +
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Residues in contact with TYR 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A LEU* 4.0 33.4 - - + +
51A SER* 4.8 2.8 + - - -
52A GLN* 4.2 1.9 + - - -
53A MET* 3.6 43.9 + - + -
7B LEU* 3.2 22.2 + - + +
8B GLN* 3.5 5.2 - - - +
9B ASP 3.2 0.4 - - - -
10B PRO* 1.3 80.3 - - - +
12B LEU* 1.3 62.2 + - + +
14B THR* 3.8 2.3 - - - -
15B LEU* 3.1 46.7 + - + +
62B VAL* 4.6 4.3 - - + -
64B PRO* 2.9 33.4 - - + +
68B VAL* 3.4 26.4 - - + +
70B LEU* 3.8 20.6 - - + +
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Residues in contact with LEU 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A MET* 3.8 21.8 - - + -
55A TYR* 4.1 5.4 - - - +
8B GLN* 2.9 44.7 + - + +
11B TYR* 1.3 78.5 - - + +
13B ASN* 1.3 57.8 + - - +
15B LEU* 3.3 13.3 + - + +
16B ARG* 2.9 29.1 + - - +
36B ILE* 4.0 23.4 - - + +
39B PHE* 3.7 39.9 - - + -
44B ILE* 4.3 12.6 - - + -
56B LYS* 4.2 8.3 - - - +
62B VAL* 4.8 4.3 - - + -
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Residues in contact with ASN 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B ASP 2.8 20.4 + - - +
10B PRO* 3.8 5.8 - - + +
12B LEU* 1.3 78.9 - - - +
14B THR* 1.3 55.9 + - - +
16B ARG* 3.1 27.1 + - - +
17B LYS* 2.9 66.8 + - - +
39B PHE* 3.6 16.0 - - + -
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Residues in contact with THR 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B PRO* 2.7 25.6 + - - +
11B TYR 3.8 3.8 - - - -
13B ASN* 1.3 73.4 - - - +
15B LEU* 1.3 65.7 + - - +
17B LYS* 4.0 5.6 - - - -
18B GLU* 3.0 50.7 + - - +
68B VAL* 4.3 15.9 - - + -
69B ARG 3.8 19.3 + - - +
70B LEU* 4.3 13.5 - - - +
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Residues in contact with LEU 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B TYR* 3.1 45.5 + - + +
12B LEU* 3.6 9.2 - - + +
14B THR* 1.3 76.0 - - - +
16B ARG* 1.3 57.4 + - - +
19B ARG* 3.1 6.9 + - - -
20B VAL* 3.0 48.5 + - + +
22B VAL* 4.0 12.3 - - + -
36B ILE* 4.1 27.7 + - + +
62B VAL* 4.2 8.3 - - + -
64B PRO* 3.7 18.8 - - + -
68B VAL* 3.4 28.0 - - + -
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Residues in contact with ARG 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B LEU 2.9 18.2 + - - +
13B ASN* 3.1 28.0 + - - +
14B THR 3.1 0.2 - - - -
15B LEU* 1.3 75.1 - - - +
17B LYS* 1.3 101.7 + - - +
19B ARG* 3.2 17.5 + - - +
36B ILE* 3.4 32.4 - - + +
37B GLU* 3.4 21.7 + - - +
38B SER* 3.9 13.9 - - - +
39B PHE* 4.2 8.5 - - - -
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Residues in contact with LYS 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B ASN* 2.9 47.6 + - - +
14B THR* 4.1 5.8 - - - +
16B ARG* 1.3 103.2 - - - +
18B GLU* 1.3 63.7 + - + +
19B ARG* 3.5 14.0 + - - +
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Residues in contact with GLU 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B THR* 3.0 40.7 + - - +
17B LYS* 1.3 80.6 - - + +
19B ARG* 1.3 73.5 + - - +
20B VAL* 3.1 14.5 + - + +
66B ARG* 2.9 29.1 + - - +
68B VAL* 5.1 1.4 - - - +
69B ARG 4.8 4.5 + - - +
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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