Contacts of the helix formed by residues 2 - 14 (chain B) 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 ALA 2 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1B MSE 1.3 78.3 - - - +
3B ALA* 1.3 66.4 + - - +
4B ALA* 3.1 14.4 - - + +
5B ALA* 3.0 9.1 + - + +
6B GLU* 3.0 19.0 + - - +
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Residues in contact with ALA 3 (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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2B ALA* 1.3 72.5 - - - +
4B ALA* 1.3 53.4 + - - +
6B GLU* 3.2 10.5 + - - +
7B LEU* 2.8 42.6 + - + +
29B GLN 4.9 6.3 + - - +
31B PRO* 3.5 36.1 - - + -
44B LEU* 4.6 11.7 - - + -
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Residues in contact with ALA 4 (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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2B ALA* 3.1 10.4 - - + +
3B ALA* 1.3 77.1 - - - +
5B ALA* 1.3 51.7 + - - +
7B LEU* 3.3 4.3 + - - +
8B SER* 2.6 35.5 + - - -
22B TYR* 3.9 37.6 - - + +
31B PRO* 4.7 2.8 - - + +
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Residues in contact with ALA 5 (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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1B MSE 3.6 27.6 - - + +
2B ALA* 3.0 16.0 + - + +
4B ALA* 1.3 75.7 - - - +
6B GLU* 1.3 65.0 + - - +
8B SER* 3.3 9.5 + - - -
9B LEU* 3.0 25.1 + - - +
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Residues in contact with GLU 6 (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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1B MSE 4.0 19.5 - - + +
2B ALA 3.0 12.6 + - - +
3B ALA* 3.5 13.2 - - - +
5B ALA* 1.3 75.8 - - - +
7B LEU* 1.3 57.7 + - - +
9B LEU* 3.2 6.5 - - - +
10B LEU* 2.9 25.4 + - + +
44B LEU* 3.9 16.0 - - + +
78B ARG* 2.4 47.9 + - - -
119B LEU* 3.7 15.5 - - + +
122B TYR* 3.5 31.7 - - + +
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Residues in contact with LEU 7 (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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3B ALA 2.8 24.6 + - - +
4B ALA 3.8 0.4 - - - +
5B ALA 3.2 0.2 - - - -
6B GLU* 1.3 70.4 - - + +
8B SER* 1.3 59.2 + - - +
10B LEU* 3.1 15.4 + - + +
11B GLU* 2.8 33.9 + - - +
22B TYR* 3.7 24.9 - - + +
31B PRO* 3.8 33.2 - - + -
44B LEU* 4.0 29.4 - - + +
47B ILE* 3.6 33.0 - - + -
48B ALA* 4.0 4.0 - - + +
51B LEU* 3.9 12.1 - - + +
119B LEU* 6.3 0.2 - - + -
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Residues in contact with SER 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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4B ALA 2.6 24.9 + - - -
5B ALA* 3.4 11.7 - - - -
7B LEU* 1.3 73.8 - - - +
9B LEU* 1.3 63.1 + - - +
11B GLU* 3.1 31.4 + - - +
12B LYS* 3.2 30.7 + - - +
22B TYR* 4.3 6.1 - - - -
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Residues in contact with LEU 9 (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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1B MSE 3.6 34.8 - - + -
5B ALA 3.0 10.0 + - - +
6B GLU 3.2 9.6 - - - +
8B SER* 1.3 76.7 - - - +
10B LEU* 1.3 62.9 + - - +
12B LYS* 3.3 6.6 + - - +
13B SER* 3.1 20.6 + - - -
122B TYR* 3.7 35.4 - - + +
156B ARG 4.6 0.7 - - - +
157B GLN* 3.2 43.2 - - + +
158B HIS* 3.4 21.8 - - + +
159B LEU* 3.9 15.0 - - + -
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Residues in contact with LEU 10 (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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6B GLU* 2.9 14.8 + - + +
7B LEU* 3.1 17.9 + - + +
9B LEU* 1.3 74.3 - - - +
11B GLU* 1.3 62.3 + - - +
13B SER* 3.4 5.4 + - - -
14B LEU* 3.1 39.7 + - + +
48B ALA* 3.4 44.9 - - + +
51B LEU* 4.3 6.7 - - + -
115B LEU* 3.8 22.0 - - + -
118B ILE* 4.0 23.8 - - + -
119B LEU* 4.5 7.2 - - + -
122B TYR* 4.0 9.6 - - + -
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Residues in contact with GLU 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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7B LEU 2.8 17.1 + - - +
8B SER* 3.1 15.0 - - - +
10B LEU* 1.3 72.2 - - - +
12B LYS* 1.3 60.3 + - + +
14B LEU* 3.3 4.9 + - - +
15B GLY 3.1 7.1 + - - -
16B LEU* 2.8 50.2 + - + +
17B SER 4.9 1.7 - - - +
18B LYS 4.0 9.6 - - - +
19B GLY* 4.5 3.1 - - - -
20B ASN* 3.4 31.5 + - - +
22B TYR* 2.3 41.2 + - - +
51B LEU* 4.0 15.7 - - + -
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Residues in contact with LYS 12 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8B SER* 3.2 33.1 + - - +
9B LEU* 3.8 8.7 - - - +
11B GLU* 1.3 75.0 - - + +
13B SER* 1.3 56.8 + - - +
14B LEU 3.1 1.1 - - - -
15B GLY* 2.7 25.0 + - - -
16B LEU 4.2 11.9 - - - +
157B GLN* 3.4 26.1 - - + +
158B HIS* 6.0 2.4 - - - -
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Residues in contact with SER 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 LEU 3.1 7.8 + - - -
10B LEU* 3.5 16.6 - - - -
12B LYS* 1.3 74.2 - - - +
14B LEU* 1.3 60.1 + - - +
15B GLY 3.6 0.2 + - - -
57B LYS* 4.4 7.1 + - - -
118B ILE* 5.0 4.5 - - - -
122B TYR* 2.8 26.8 + - - -
153B PRO 5.4 2.1 - - - +
154B GLY* 3.2 24.8 + - - -
155B ILE* 3.7 23.0 - - - +
157B GLN* 3.5 3.1 + - - -
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Residues in contact with LEU 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 LEU* 3.1 32.5 + - + +
11B GLU 3.6 7.6 - - - +
12B LYS 3.1 1.2 - - - -
13B SER* 1.3 77.3 - - - +
15B GLY* 1.3 60.4 + - - +
16B LEU* 3.4 6.0 + - + -
51B LEU* 3.5 43.7 - - + +
52B VAL* 3.6 17.0 - - + +
55B ALA* 3.6 19.9 - - + +
57B LYS* 3.6 29.0 + - + +
60B LEU* 3.4 32.8 - - + -
118B ILE* 5.2 4.3 - - + -
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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