Contacts of the helix formed by residues 7 - 19 (chain L) in PDB entry 6T9L
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 GLN 7 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5L THR* 3.6 22.0 + - + +
6L ALA* 1.3 76.1 - - - +
8L LEU* 1.3 61.8 + - - +
10L SER* 2.7 25.4 + - - +
11L GLN* 3.3 26.2 + - + +
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Residues in contact with LEU 8 (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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5L THR* 3.6 30.4 - - + +
6L ALA 3.3 1.4 - - - -
7L GLN* 1.3 78.1 - - - +
9L LYS* 1.3 79.7 + - + +
10L SER 3.3 0.9 + - - -
11L GLN* 3.3 13.6 + - - +
12L ILE* 3.5 23.1 + - + +
6M ILE* 4.3 23.3 - - + -
11M ILE* 4.0 26.9 - - + -
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Residues in contact with LYS 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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51K GLU* 4.7 20.4 - - + +
5L THR 4.9 3.4 + - - +
6L ALA 4.2 6.0 + - - +
7L GLN 3.5 0.2 - - - -
8L LEU* 1.3 89.8 - - + +
10L SER* 1.3 61.4 + - - +
12L ILE* 3.2 28.1 - - + +
13L GLN* 3.2 25.9 - - - +
11M ILE* 4.4 29.2 - - + +
14M GLY* 6.3 3.4 - - - -
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Residues in contact with SER 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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49K CYS 5.1 3.6 - - - -
50K HIS* 4.7 21.8 - - - -
6L ALA 4.4 4.9 + - - -
7L GLN* 2.7 36.3 + - - +
9L LYS* 1.3 78.1 - - - +
11L GLN* 1.3 63.2 + - - +
13L GLN* 3.4 9.4 + - - +
14L GLN* 2.8 30.4 + - - +
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Residues in contact with GLN 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 GLN* 3.3 24.4 + - + +
8L LEU* 3.3 8.6 + - - +
10L SER* 1.3 81.5 + - - +
12L ILE* 1.3 57.8 + - + +
14L GLN* 3.1 27.3 + - - +
15L TYR* 2.9 31.2 + - - +
11N ILE* 5.6 12.1 - - + -
15N VAL* 4.5 15.1 - - + +
16N ILE* 4.9 14.5 - - - +
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Residues in contact with ILE 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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8L LEU* 3.5 15.9 + - + +
9L LYS* 3.2 30.5 - - + +
11L GLN* 1.3 77.5 - - + +
13L GLN* 1.3 65.2 + - + +
15L TYR* 3.7 5.2 + - - +
16L LEU* 3.1 30.3 + - - +
89L LEU* 5.5 11.9 - - + -
92L ILE* 5.7 6.3 - - + -
93L VAL* 5.6 7.9 - - + -
11M ILE* 3.7 30.7 - - + -
15M ILE* 4.6 13.2 - - + -
11N ILE* 5.5 11.4 - - + -
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Residues in contact with GLN 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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41K LEU* 5.4 0.4 - - - +
50K HIS 3.7 4.5 - - - +
51K GLU* 3.5 14.7 - - - +
52K ILE* 3.0 56.5 + - + +
9L LYS* 3.2 25.3 + - - +
10L SER* 3.4 4.6 + - - +
11L GLN 3.3 0.2 - - - -
12L ILE* 1.3 82.6 - - + +
14L GLN* 1.3 63.4 + - - +
16L LEU* 3.9 11.7 - - + +
17L VAL* 3.5 21.5 + - - +
22L TYR* 5.5 6.6 - - + -
15M ILE* 5.3 13.0 - - + +
18M ASN* 4.0 21.6 - - - +
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Residues in contact with GLN 14 (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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41K LEU* 5.1 13.0 - - + -
45K LYS* 6.2 1.3 - - - +
10L SER 2.8 17.7 + - - +
11L GLN* 3.1 35.1 + - - +
13L GLN* 1.3 77.3 - - - +
15L TYR* 1.3 63.5 + - - +
17L VAL* 3.2 21.7 - - - +
18L GLU* 3.2 30.5 + - + +
15N VAL* 5.6 3.8 - - - +
20N SER 2.4 38.4 + - - -
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Residues in contact with TYR 15 (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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11L GLN 2.9 15.6 + - - +
12L ILE* 4.3 4.0 - - - +
14L GLN* 1.3 74.6 - - - +
16L LEU* 1.3 56.1 + - + +
18L GLU* 3.6 9.6 - - - -
19L SER* 2.5 64.1 + - - -
21L ASN* 5.5 0.7 - - - -
88L PHE 5.8 2.2 - - - -
91L GLU* 5.0 17.0 + - + +
92L ILE* 4.5 25.3 - - + +
14N LYS* 4.5 13.4 + - - -
15N VAL* 3.8 36.5 - - + +
19N TYR* 3.6 36.1 + + - -
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Residues in contact with LEU 16 (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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12L ILE 3.1 20.5 + - - +
13L GLN* 3.9 11.2 - - + +
14L GLN 3.2 0.8 - - - -
15L TYR* 1.3 81.8 - - + +
17L VAL* 1.3 57.1 + - - +
19L SER* 3.3 4.4 + - - +
21L ASN* 3.1 44.2 + - + +
22L TYR* 3.0 53.0 + - + +
25L ILE* 3.8 16.6 - - + -
88L PHE* 5.0 12.6 - - + +
89L LEU* 5.8 8.5 - - + -
15M ILE* 5.3 15.9 - - + -
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Residues in contact with VAL 17 (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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36K PRO 4.6 0.2 - - - +
37K LYS* 3.7 46.3 - - + +
40K PHE* 4.3 18.2 - - + -
41K LEU* 4.0 26.2 - - + -
52K ILE* 6.4 0.9 - - + -
13L GLN 3.5 12.0 + - - +
14L GLN 3.2 17.0 - - - +
16L LEU* 1.3 76.5 - - - +
18L GLU* 1.3 66.5 + - + +
20L GLY* 3.2 11.4 + - - -
22L TYR* 3.8 19.0 - - + +
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Residues in contact with GLU 18 (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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37K LYS* 4.8 11.1 - - - +
41K LEU* 5.7 7.4 - - + +
14L GLN* 3.2 45.9 + - + +
15L TYR* 3.3 15.0 + - + +
17L VAL* 1.3 82.1 - - + +
19L SER* 1.3 60.7 + - - +
20L GLY* 3.1 1.6 + - - -
15N VAL* 4.4 2.8 - - - +
19N TYR* 3.6 59.7 + - + +
20N SER 4.0 1.4 - - - -
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Residues in contact with SER 19 (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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15L TYR* 2.5 55.0 + - - -
16L LEU* 3.3 10.6 + - - +
18L GLU* 1.3 73.1 - - - +
20L GLY* 1.3 58.9 + - - +
21L ASN* 3.5 25.4 + - - +
19N TYR* 4.5 9.0 - - - -
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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