Contacts of the helix formed by residues 1 - 14 (chain A) in PDB entry 2UZ8
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 MSE 1 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A ALA* 1.3 67.5 + - - +
3A ALA 3.4 3.3 + - - -
4A ALA* 3.4 17.9 + - + +
5A ALA* 3.6 11.7 + - - +
29A GLN* 3.4 38.8 + - - +
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Residues in contact with ALA 2 (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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1A MSE 1.3 76.4 - - - +
3A ALA* 1.3 57.5 + - - +
5A ALA* 3.4 8.3 + - - +
6A GLU* 2.9 30.0 + - - +
29A GLN* 4.8 1.4 + - - -
126A ARG* 6.5 0.9 - - - -
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Residues in contact with ALA 3 (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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1A MSE 3.4 0.6 - - - -
2A ALA* 1.3 75.8 - - - +
4A ALA* 1.3 60.3 + - - +
6A GLU* 3.3 8.9 + - - +
7A LEU* 3.0 34.5 + - - +
29A GLN 4.7 8.1 - - - +
31A PRO* 4.0 31.6 - - + -
44A LEU* 4.2 12.1 - - + +
78A ARG* 6.3 0.4 - - - +
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Residues in contact with ALA 4 (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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1A MSE 3.4 13.3 + - + +
2A ALA 3.4 0.4 - - - -
3A ALA* 1.3 77.9 - - - +
5A ALA* 1.3 58.4 + - - +
7A LEU* 3.3 2.7 + - - -
8A SER* 3.0 31.1 + - - -
22A TYR* 3.7 44.4 - - + +
23A SER 5.6 1.8 - - - +
31A PRO* 4.8 2.8 - - + +
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Residues in contact with ALA 5 (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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1A MSE 3.6 8.8 + - - +
2A ALA* 3.4 10.9 + - - +
3A ALA 3.3 0.2 - - - -
4A ALA* 1.3 75.5 - - - +
6A GLU* 1.3 60.5 + - - +
8A SER* 3.2 10.2 + - - -
9A LEU* 2.9 28.6 + - - +
158A HIS* 5.4 4.4 - - + -
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Residues in contact with GLU 6 (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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2A ALA* 2.9 18.6 + - - +
3A ALA* 3.6 8.0 - - - +
4A ALA 3.3 0.4 - - - -
5A ALA* 1.3 77.8 - - - +
7A LEU* 1.3 57.5 + - - +
9A LEU* 3.2 13.9 - - + +
10A LEU* 3.0 25.3 + - - +
44A LEU* 3.8 17.0 - - + +
78A ARG* 2.4 47.9 + - - -
119A LEU* 4.0 10.5 - - + +
122A TYR* 3.5 33.7 - - + +
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Residues in contact with LEU 7 (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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3A ALA 3.0 20.0 + - - +
4A ALA 3.3 0.6 + - - +
5A ALA 3.3 0.2 - - - -
6A GLU* 1.3 74.6 - - - +
8A SER* 1.3 60.4 + - - +
10A LEU* 3.8 7.2 - - + +
11A GLU* 3.0 34.2 + - - +
22A TYR* 3.7 24.7 - - + +
31A PRO* 3.9 18.8 - - + -
44A LEU* 3.8 21.3 - - + +
47A ILE* 3.8 47.3 - - + -
48A ALA* 3.8 19.7 - - + +
51A LEU* 3.8 13.1 - - + +
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Residues in contact with SER 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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4A ALA 3.0 14.9 + - - -
5A ALA* 3.2 14.3 + - - -
7A LEU* 1.3 74.5 - - - +
9A LEU* 1.3 66.8 + - - +
11A GLU* 3.2 19.9 + - - +
12A LYS* 3.2 34.4 + - - +
20A ASN 4.9 3.8 + - - -
22A TYR* 4.3 8.5 - - - -
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Residues in contact with LEU 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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5A ALA 2.9 11.7 + - - +
6A GLU* 3.2 17.3 - - + +
8A SER* 1.3 75.2 - - - +
10A LEU* 1.3 56.7 + - - +
12A LYS* 3.1 12.1 + - + +
13A SER* 2.9 26.4 + - - -
122A TYR* 3.7 27.8 - - + +
156A ARG 4.2 6.3 - - - +
157A GLN* 3.6 26.7 - - + -
158A HIS* 3.5 33.3 - - + +
159A LEU* 3.9 33.2 - - + -
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Residues in contact with LEU 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 GLU* 3.0 16.0 + - + +
7A LEU* 3.4 9.8 + - + +
8A SER 3.3 0.4 - - - -
9A LEU* 1.3 72.7 - - - +
11A GLU* 1.3 66.1 + - - +
13A SER* 3.2 9.5 + - - +
14A LEU* 2.9 42.4 + - + +
48A ALA* 3.5 42.8 - - + +
51A LEU* 4.0 12.6 - - + -
115A LEU* 3.9 17.0 - - + -
118A ILE* 3.8 29.6 - - + -
119A LEU* 4.4 6.5 - - + -
122A TYR* 4.1 7.9 - - + -
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Residues in contact with GLU 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 20.5 + - - +
8A SER* 3.2 20.2 + - - +
10A LEU* 1.3 79.2 - - - +
12A LYS* 1.3 62.4 + - + +
14A LEU* 3.3 2.5 + - - +
15A GLY 3.2 3.6 + - - -
16A LEU* 3.0 50.3 + - + +
18A LYS 4.7 2.2 - - - +
19A GLY* 3.4 20.5 - - - -
20A ASN* 3.3 23.5 + - - +
22A TYR* 2.5 32.7 + - - +
51A LEU* 4.2 16.6 - - + +
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Residues in contact with LYS 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 SER* 3.2 20.5 + - - +
9A LEU* 3.1 13.1 + - + +
11A GLU* 1.3 79.9 - - + +
13A SER* 1.3 63.9 + - - +
15A GLY* 3.1 13.3 + - - -
16A LEU 4.8 7.2 - - - +
157A GLN* 3.6 31.8 + - + +
158A HIS* 5.4 9.2 + - + +
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Residues in contact with SER 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 LEU 2.9 6.3 + - - -
10A LEU* 3.2 23.0 + - - +
12A LYS* 1.3 75.7 - - - +
14A LEU* 1.3 58.5 + - - +
15A GLY 3.3 1.0 + - - -
57A LYS* 4.4 6.4 + - - -
118A ILE* 4.5 2.1 - - - +
122A TYR* 2.7 28.4 + - - -
153A PRO 5.2 1.2 - - - +
154A GLY* 3.0 32.0 - - - +
155A ILE* 3.9 20.9 - - - +
157A GLN* 3.8 1.9 - - - +
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Residues in contact with LEU 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 LEU* 2.9 40.9 + - + +
11A GLU 3.7 4.7 - - - +
13A SER* 1.3 77.9 - - - +
15A GLY* 1.3 63.7 + - - +
16A LEU* 4.4 5.8 - - + -
51A LEU* 3.6 43.1 - - + +
52A VAL* 3.7 14.4 - - + +
55A ALA* 3.8 19.2 - - + +
57A LYS* 3.3 31.4 + - + +
60A LEU* 3.6 31.2 - - + -
118A ILE* 5.1 3.6 - - + -
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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