Contacts of the helix formed by residues 3 - 14 (chain B) in PDB entry 2PCB
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 VAL 3 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1B GLY 5.3 0.7 - - - +
2B ASP* 1.3 71.4 - - + +
4B GLU* 1.3 67.3 - - + +
6B GLY 3.3 1.3 - - - -
7B LYS* 2.5 36.0 + - - +
96B ALA* 3.5 9.2 - - + -
97B TYR* 3.0 45.1 - - + +
100B LYS* 3.3 40.4 - - + +
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Residues in contact with GLU 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 ASP* 3.4 18.8 - - + +
3B VAL* 1.3 94.7 - - + +
5B LYS* 1.3 65.4 - - + +
7B LYS* 3.0 19.1 - - - +
8B LYS* 3.6 14.8 + - - +
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Residues in contact with LYS 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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35A GLU* 4.7 14.9 + - - +
39A TYR* 4.3 15.7 + - - +
2B ASP* 3.2 20.5 + - - +
4B GLU* 1.3 85.6 - - + +
6B GLY* 1.3 61.8 + - - +
7B LYS 3.2 0.5 + - - -
8B LYS* 3.4 25.2 + - + +
9B ILE* 3.4 17.0 + - - +
93B ASP* 3.1 26.7 - - - +
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Residues in contact with GLY 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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2B ASP 2.9 13.4 + - - -
3B VAL 3.1 2.0 + - - -
4B GLU 3.0 0.6 - - - -
5B LYS* 1.3 80.8 - - - +
7B LYS* 1.3 59.0 + - - +
9B ILE* 3.5 7.1 + - - +
10B PHE 3.4 14.6 + - - -
93B ASP* 3.1 33.2 - - - -
94B LEU* 3.8 6.5 - - - +
97B TYR* 3.5 14.0 - - - +
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Residues in contact with LYS 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 VAL 2.5 20.5 + - - +
4B GLU* 3.0 10.8 - - - +
6B GLY* 1.3 71.6 - - - +
8B LYS* 1.3 73.5 + - + +
10B PHE* 3.2 4.9 + - - +
11B VAL* 3.1 47.3 + - + +
97B TYR* 3.4 31.0 - - + +
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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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38A ASN* 3.0 34.9 + - + +
39A TYR* 3.8 22.7 - - + -
4B GLU* 3.6 14.5 + - - +
5B LYS* 3.4 18.1 + - + +
6B GLY 3.4 0.2 - - - -
7B LYS* 1.3 87.1 - - + +
9B ILE* 1.4 65.3 + - - +
11B VAL* 3.3 7.7 + - - +
12B GLN* 3.0 27.0 + - - +
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Residues in contact with ILE 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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39A TYR* 3.6 28.9 - - + +
5B LYS 3.4 9.8 + - - +
6B GLY 3.5 7.9 - - - +
7B LYS 3.2 0.4 - - - -
8B LYS* 1.4 79.5 - - - +
10B PHE* 1.3 51.8 + - - +
12B GLN* 3.7 0.2 - - - +
13B LYS* 2.8 42.2 + - + +
14B CYS* 4.1 0.2 - - - -
85B ILE* 3.9 11.2 - - + -
90B GLU* 2.7 59.2 - - + +
93B ASP* 4.0 15.0 - - + -
94B LEU* 3.3 34.5 - - + +
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Residues in contact with PHE 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 GLY 3.4 5.4 + - - +
7B LYS 3.2 8.4 + - - +
8B LYS 3.2 0.4 - - - -
9B ILE* 1.3 76.8 - - - +
11B VAL* 1.3 65.7 + - + +
14B CYS* 3.1 29.4 + - + -
15B ALA* 2.7 62.1 + - + -
18B HIS* 3.5 22.0 - - + -
20B VAL* 3.4 37.2 - - + -
32B LEU* 4.6 11.0 - - + -
94B LEU* 4.0 6.5 - - + -
97B TYR* 3.9 24.2 - + + -
98B LEU* 4.2 21.1 - - + -
105B HEM 5.2 2.0 - - + -
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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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7B LYS* 3.1 41.0 + - + +
8B LYS* 3.8 7.0 - - - +
10B PHE* 1.3 82.5 - - + +
12B GLN* 1.3 66.0 + - + +
15B ALA* 3.5 15.4 - - + +
16B GLN* 3.0 25.1 - - - +
97B TYR* 6.0 1.3 - - - +
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Residues in contact with GLN 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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38A ASN* 3.8 9.3 + - - +
39A TYR* 3.3 36.8 - - + +
40A ILE* 3.8 24.0 - - - +
193A ALA 4.5 4.1 - - - +
194A ALA* 5.0 1.7 - - - -
195A ASN* 3.3 30.0 + - - +
196A ASN* 4.2 13.4 - - - +
8B LYS 3.0 18.3 + - - +
9B ILE 3.7 2.5 - - - +
11B VAL* 1.3 85.1 - - + +
13B LYS* 1.3 55.7 + - + +
16B GLN* 2.7 18.6 + - - -
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Residues in contact with LYS 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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34A ASP* 3.5 19.2 + - - +
39A TYR* 3.8 26.7 + - + -
196A ASN* 4.5 11.4 - - - +
9B ILE* 2.8 27.9 + - + +
12B GLN* 1.3 83.2 - - + +
14B CYS* 1.3 51.1 + - - +
16B GLN* 2.9 8.1 + - - +
82B PHE* 3.8 18.1 - - + -
85B ILE* 4.6 6.7 - - + +
90B GLU* 2.7 31.5 + - - +
105B HEM 2.8 46.0 - - + +
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Residues in contact with CYS 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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9B ILE 4.1 2.9 - - - -
10B PHE* 3.1 44.8 + - + -
13B LYS* 1.3 76.4 - - - +
15B ALA* 1.3 52.7 + - - +
16B GLN* 2.6 9.0 - - - +
17B CYS* 2.5 34.5 + - - +
18B HIS* 3.4 6.2 + - + -
94B LEU* 4.2 5.2 - - - -
105B HEM 2.3 61.0 - - + -
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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