Contacts of the helix formed by residues 4 - 16 (chain B) in PDB entry 1NEJ
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 THR 4 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3B LEU* 1.3 72.3 - - - +
5B PRO* 1.4 67.1 - - - +
6B VAL* 3.2 18.7 - - + +
7B GLU* 2.8 54.4 + - + +
8B LYS* 2.9 11.4 + - - +
132B LYS* 4.6 4.6 - - - +
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Residues in contact with PRO 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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3B LEU 3.8 3.8 - - - +
4B THR* 1.4 87.0 - - - +
6B VAL* 1.3 59.2 + - - +
8B LYS* 3.7 9.9 - - + +
9B SER* 2.9 30.5 + - - -
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Residues in contact with VAL 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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4B THR* 3.5 25.3 + - + +
5B PRO* 1.3 76.6 - - - +
7B GLU* 1.3 69.2 + - + +
9B SER* 3.3 6.0 + - - -
10B ALA* 2.9 31.7 + - + +
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Residues in contact with GLU 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A LEU* 5.7 1.9 - - - +
3B LEU* 4.1 7.4 - - + +
4B THR* 2.8 27.7 + - + +
6B VAL* 1.3 82.8 - - + +
8B LYS* 1.3 63.9 + - - +
10B ALA* 3.9 7.0 - - + +
11B VAL* 3.2 30.3 + - - +
125B PRO* 3.6 22.0 - - + +
128B ALA* 4.2 8.0 - - - +
129B ALA* 3.9 23.3 + - + +
132B LYS* 2.7 36.6 + - - +
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Residues in contact with LYS 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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3B LEU* 3.9 25.5 - - + +
4B THR 2.9 12.1 + - - +
5B PRO* 3.7 13.7 - - + +
6B VAL 3.3 0.2 - - - -
7B GLU* 1.3 76.3 - - - +
9B SER* 1.3 54.5 + - - +
11B VAL* 3.2 15.0 - - + +
12B THR* 2.6 44.1 + - - +
75B LEU 4.2 19.6 + - - -
76B ALA* 5.5 3.6 + - - +
78B LEU* 4.6 11.0 - - + -
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Residues in contact with SER 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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5B PRO 2.9 18.8 + - - -
6B VAL* 3.6 5.6 - - - -
7B GLU 3.2 0.2 - - - -
8B LYS* 1.3 77.6 - - - +
10B ALA* 1.3 58.8 + - - +
12B THR* 3.4 6.6 + - - -
13B ALA* 3.1 30.1 + - - +
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Residues in contact with ALA 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 VAL* 2.9 20.7 + - + +
7B GLU* 3.9 10.3 - - + +
8B LYS 3.4 0.2 - - - -
9B SER* 1.3 78.3 - - - +
11B VAL* 1.3 58.9 + - + +
13B ALA* 4.3 4.4 - - - +
14B LEU* 3.3 24.6 + - - +
126B VAL* 4.5 25.6 - - + +
129B ALA* 5.6 0.4 - - + -
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Residues in contact with VAL 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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3B LEU* 5.1 7.0 - - + -
7B GLU 3.2 14.5 + - - +
8B LYS* 3.2 20.6 - - + +
10B ALA* 1.3 77.4 - - - +
12B THR* 1.3 65.8 + - - +
13B ALA 3.3 0.2 - - - -
15B TRP* 2.8 34.6 + - - +
75B LEU* 4.0 21.5 - - + -
78B LEU* 5.4 2.9 - - + -
126B VAL* 4.5 1.3 - - + +
129B ALA* 3.5 31.6 - - + +
130B TYR* 3.1 33.7 + - + -
133B VAL* 5.0 1.6 - - + -
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Residues in contact with THR 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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8B LYS* 2.6 41.0 + - - +
9B SER* 3.4 7.7 + - - -
11B VAL* 1.3 80.8 - - - +
13B ALA* 1.3 52.2 + - - +
15B TRP* 3.7 4.8 - - - +
16B GLY* 2.8 29.6 + - - -
75B LEU* 6.0 1.1 - - - +
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Residues in contact with ALA 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 SER 3.1 17.1 + - - +
10B ALA* 4.3 4.7 - - - +
11B VAL 3.3 0.2 - - - -
12B THR* 1.3 75.0 - - - +
14B LEU* 1.3 62.2 + - - +
16B GLY* 3.3 9.1 + - - -
17B LYS* 3.4 22.4 + - - +
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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 ALA 3.3 18.8 + - - +
11B VAL 3.7 3.6 - - - +
13B ALA* 1.3 74.8 - - - +
15B TRP* 1.3 65.1 + - - +
17B LYS* 3.2 10.7 + - - +
18B VAL* 3.5 0.9 + - - -
114B LEU* 4.5 6.5 - - + -
118B PHE* 3.4 62.4 - - + -
121B GLU* 4.1 31.2 - - + +
122B PHE* 4.4 6.7 - - + -
126B VAL* 4.0 11.4 - - + -
130B TYR* 3.6 28.9 - - + +
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Residues in contact with TRP 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 VAL 2.8 19.4 + - - +
12B THR* 3.7 5.2 - - - +
14B LEU* 1.3 72.2 - - - +
16B GLY* 1.3 57.8 + - - +
17B LYS 3.0 4.9 - - - -
18B VAL* 3.0 44.2 + - + +
68B LEU* 3.6 36.8 - - + -
71B PHE* 4.1 12.3 - + + -
72B SER* 2.9 34.9 + - - -
75B LEU* 3.6 24.0 - - + +
110B LEU* 4.1 17.0 - - + -
114B LEU* 3.9 27.8 - - + -
130B TYR* 3.0 40.3 + + - +
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Residues in contact with GLY 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 THR 2.8 19.6 + - - -
13B ALA* 3.6 6.5 - - - -
14B LEU 3.1 1.0 - - - -
15B TRP* 1.3 76.9 - - - +
17B LYS* 1.3 59.3 + - - +
18B VAL 3.5 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