Contacts of the helix formed by residues 3 - 15 (chain L) in PDB entry 6CP3
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 3 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1K FME 6.0 1.8 - - - -
3K LEU* 3.8 29.6 - - + -
1L FME 3.0 11.5 + - - +
2L GLN* 1.3 81.9 - - - +
4L VAL* 1.3 63.9 + - - +
5L LEU 3.2 2.7 - - - -
6L ALA* 3.3 6.2 + - + +
7L ALA* 3.1 21.0 + - + +
3M LEU* 3.7 30.3 - - + -
6M ALA* 4.6 6.7 - - + -
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Residues in contact with VAL 4 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1L FME 2.7 40.4 + - + +
3L LEU* 1.3 74.3 - - - +
5L LEU* 1.3 61.7 + - + +
7L ALA* 3.3 7.6 + - - +
8L LYS* 2.9 29.5 + - + +
5M LEU* 3.9 15.5 - - + -
6M ALA* 3.7 23.8 - - + +
9M TYR* 3.6 35.0 - - + -
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Residues in contact with LEU 5 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1K FME 5.1 0.2 - - - +
4K VAL* 3.8 20.4 - - + -
1L FME 3.4 15.9 - - - +
2L GLN* 3.3 28.5 - - - +
3L LEU 3.2 1.4 - - - -
4L VAL* 1.3 80.7 - - + +
6L ALA* 1.3 60.3 + - - +
8L LYS* 3.2 8.3 + - - +
9L TYR* 2.9 63.5 + - + +
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Residues in contact with ALA 6 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3K LEU* 3.8 17.7 - - + -
4K VAL* 3.8 27.6 - - + -
7K ALA* 3.8 14.6 - - + -
3L LEU* 3.3 9.5 + - + +
5L LEU* 1.3 78.4 - - - +
7L ALA* 1.3 60.4 - - - +
9L TYR* 3.2 13.1 + - - +
10L ILE* 3.0 33.4 + - - +
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Residues in contact with ALA 7 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3L LEU* 3.1 16.1 + - + +
4L VAL 3.4 8.7 - - - +
6L ALA* 1.3 77.9 - - - +
8L LYS* 1.3 58.9 + - + +
10L ILE* 3.4 9.0 - - - +
11L GLY* 2.8 22.7 + - - -
6M ALA* 3.7 30.1 - - + +
9M TYR* 5.4 0.2 - - - -
10M ILE* 3.3 26.2 - - + +
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Residues in contact with LYS 8 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4L VAL* 2.9 23.5 + - + +
5L LEU* 3.2 7.6 + - - +
7L ALA* 1.3 74.2 - - - +
9L TYR* 1.3 63.9 + - + +
11L GLY 4.1 0.4 - - - +
12L ALA* 2.9 24.1 + - - +
71L LEU 4.3 4.1 + - - -
72L LEU* 2.9 52.3 - - + +
73L LEU* 4.8 4.1 - - - -
74L PHE 4.3 19.8 + - - -
9M TYR* 3.6 38.5 - - + -
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Residues in contact with TYR 9 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4K VAL* 3.2 30.3 - - + -
5K LEU* 6.4 0.2 - - + -
7K ALA* 4.8 1.6 - - + -
8K LYS* 4.0 27.6 - - + +
11K GLY* 5.2 0.4 - - - -
72K LEU* 3.8 22.7 - - + +
5L LEU* 2.9 56.8 + - + +
6L ALA* 3.2 11.9 + - - +
8L LYS* 1.3 78.6 - - + +
10L ILE* 1.3 58.4 + - - +
12L ALA* 3.2 8.4 + - - +
13L GLY* 3.0 20.1 + - - -
73L LEU* 4.1 25.8 - - + -
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Residues in contact with ILE 10 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7K ALA* 3.3 39.9 - - + +
10K ILE* 3.7 26.0 - - + -
11K GLY* 4.3 4.0 - - - +
14K ILE* 5.2 0.6 - - + +
6L ALA 3.0 15.4 + - - +
7L ALA* 3.4 7.9 - - - +
9L TYR* 1.3 73.2 - - - +
11L GLY* 1.3 60.0 + - - +
13L GLY* 3.4 3.9 - - - +
14L ILE* 2.9 41.4 + - + +
10M ILE* 3.7 30.5 - - + -
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Residues in contact with GLY 11 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7L ALA 2.8 19.2 + - - -
8L LYS 3.7 0.9 - - - -
9L TYR 3.2 0.4 - - - -
10L ILE* 1.3 77.3 - - - +
12L ALA* 1.3 58.8 + - - +
14L ILE* 3.3 15.7 - - - +
15L SER* 2.8 31.4 + - - -
72L LEU* 3.4 22.2 - - - +
10M ILE* 4.7 3.8 - - - -
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Residues in contact with ALA 12 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15K SER* 4.6 0.2 - - - -
68K VAL* 5.3 2.0 - - + +
72K LEU* 4.5 12.7 - - + +
8L LYS 2.9 14.3 + - - +
9L TYR* 3.5 10.8 - - - +
11L GLY* 1.3 74.4 - - - +
13L GLY* 1.3 52.0 + - - +
15L SER* 3.5 10.4 + - - -
16L THR* 2.4 27.0 + - - -
69L SER* 3.2 35.6 + - - +
72L LEU* 3.9 2.1 - - - +
73L LEU* 4.3 15.3 - - + -
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Residues in contact with GLY 13 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11K GLY* 3.7 13.5 - - - -
14K ILE* 4.0 8.8 - - - +
15K SER* 3.7 24.1 + - - -
72K LEU* 4.0 2.0 - - - +
9L TYR 3.0 13.6 + - - -
10L ILE 3.2 5.3 + - - -
11L GLY 3.2 0.4 - - - -
12L ALA* 1.3 77.2 - - - +
14L ILE* 1.3 59.6 + - - +
16L THR* 2.7 22.1 + - - -
17L ILE* 5.0 1.2 + - - +
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Residues in contact with ILE 14 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10K ILE* 6.4 0.2 - - + -
14K ILE* 3.7 23.6 - - + -
10L ILE* 2.9 33.3 + - + +
11L GLY* 3.3 17.0 - - - +
13L GLY* 1.3 72.9 - - - +
15L SER* 1.3 54.9 + - - +
16L THR 3.3 2.3 + - - -
17L ILE* 4.5 5.2 - - - +
10M ILE* 3.3 36.6 - - + +
13M GLY* 3.5 13.8 - - - +
14M ILE* 3.7 23.2 - - + -
17M ILE* 3.4 21.1 - - - +
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Residues in contact with SER 15 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11L GLY 2.8 22.0 + - - -
12L ALA* 3.5 2.9 + - - -
13L GLY 3.2 0.6 - - - -
14L ILE* 1.3 76.7 - - - +
16L THR* 1.3 58.0 + - - +
65L CYS* 3.2 18.9 - - - +
66L LEU* 4.6 0.2 - - - -
68L VAL* 4.8 1.1 - - - -
69L SER* 3.3 36.0 - - - -
72L LEU* 4.3 4.5 - - - +
13M GLY* 3.8 7.6 - - - -
16M THR* 3.6 33.4 - - - -
17M ILE* 4.2 1.6 - - - -
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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