Contacts of the helix formed by residues 14 - 23 (chain L) in PDB entry 6IY6
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 PRO 14 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6L LEU* 5.8 0.7 - - + -
8L VAL* 3.8 28.0 - - + -
9L ASN 4.3 0.2 - - - +
12L ASP 3.6 2.4 - - - +
13L PRO* 1.4 80.4 - - + +
15L LEU* 1.3 64.5 + - - +
16L GLY 3.3 2.2 - - - -
17L ALA* 3.2 26.9 + - + -
18L LEU* 3.3 14.5 + - + +
38L ASN* 3.4 43.1 - - + +
51L VAL* 4.5 13.5 - - + -
54L ILE* 6.3 1.6 - - + -
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Residues in contact with LEU 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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13L PRO* 3.0 11.4 + - + +
14L PRO* 1.3 69.2 - - - +
16L GLY* 1.3 62.4 + - - +
18L LEU* 3.4 14.9 + - + +
19L LEU* 3.2 43.8 + - + +
125L TRP* 4.1 10.5 - - + -
126L ALA* 3.6 36.1 - - + +
129L LYS* 4.0 20.9 - - + -
130L GLY* 5.0 2.5 - - - +
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Residues in contact with GLY 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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14L PRO 3.3 0.8 - - - -
15L LEU* 1.3 75.9 - - - +
17L ALA* 1.3 57.8 + - - +
19L LEU* 3.4 9.0 + - - +
20L ALA* 3.0 28.9 + - - +
51L VAL* 6.3 0.4 - - - -
55L LEU* 3.8 11.5 - - - +
122L LEU* 4.5 11.5 - - - +
123L CYS* 5.1 2.7 - - - -
126L ALA* 3.3 24.0 - - - +
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Residues in contact with ALA 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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6L LEU* 4.8 8.1 - - + -
14L PRO* 3.2 30.5 + - + +
16L GLY* 1.3 71.3 - - - +
18L LEU* 1.3 55.3 + - - +
20L ALA* 3.1 5.4 + - - +
21L VAL* 2.8 39.2 + - - +
51L VAL* 4.9 8.9 - - + +
54L ILE* 4.7 19.5 - - + -
55L LEU* 3.8 18.5 - - + +
58L LEU* 4.4 1.4 - - - +
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Residues in contact with LEU 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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6L LEU* 4.9 5.4 - - + -
8L VAL* 4.0 32.1 - - + -
13L PRO* 4.2 23.3 - - + -
14L PRO* 3.3 15.4 + - + +
15L LEU* 3.5 13.9 - - + +
17L ALA* 1.3 71.8 - - - +
19L LEU* 1.3 56.7 + - + +
21L VAL* 3.0 10.2 + - + +
22L GLU* 2.9 42.8 + - + +
32L VAL* 4.9 14.6 - - + -
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Residues in contact with LEU 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 LEU* 3.2 29.8 + - + +
16L GLY* 3.5 13.2 - - - +
18L LEU* 1.3 75.2 - - + +
20L ALA* 1.3 59.3 + - - +
22L GLU* 3.4 19.1 + - - +
23L HIS* 2.7 31.2 + - + -
122L LEU* 4.3 18.6 - - + +
125L TRP* 3.7 34.3 - - + -
126L ALA* 4.5 2.2 - - + -
158L LEU* 3.9 39.9 - - + +
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Residues in contact with ALA 20 (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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16L GLY 3.0 13.6 + - - +
17L ALA 3.2 9.0 - - - +
19L LEU* 1.3 73.2 - - - +
21L VAL* 1.3 60.1 + - - +
23L HIS* 2.9 21.1 + - - +
24L VAL* 3.2 19.3 + - + +
55L LEU* 4.0 17.3 - - + -
58L LEU* 4.3 14.1 - - + -
67L LEU* 5.0 3.6 - - + -
119L LEU* 4.6 8.3 - - + -
122L LEU* 3.8 17.9 - - + +
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Residues in contact with VAL 21 (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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6L LEU* 3.6 29.2 - - + -
17L ALA 2.8 21.2 + - - +
18L LEU* 3.3 11.7 - - + +
20L ALA* 1.3 71.9 - - - +
22L GLU* 1.3 62.7 + - + +
24L VAL* 3.2 22.3 - - - +
25L LYS* 3.2 24.6 + - - +
30L ILE* 3.9 26.7 - - + -
32L VAL* 3.7 26.7 - - + -
58L LEU* 4.0 9.2 - - + -
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Residues in contact with GLU 22 (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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18L LEU* 2.9 21.0 + - + +
19L LEU* 3.6 22.1 - - - +
20L ALA 3.2 0.2 - - - -
21L VAL* 1.3 76.5 - - + +
23L HIS* 1.3 66.1 + - + +
24L VAL 3.4 0.4 + - - -
25L LYS* 4.0 33.0 + - - +
26L ASP 5.1 0.9 + - - -
158L LEU 5.0 5.0 - - - +
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Residues in contact with HIS 23 (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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19L LEU* 2.7 24.1 + - + +
20L ALA* 2.9 10.5 + - - +
22L GLU* 1.3 82.9 - - + +
24L VAL* 1.3 60.5 + - - +
25L LYS 3.7 0.4 - - - -
26L ASP* 4.9 8.2 + - - +
27L ASP* 5.4 0.5 + - - +
65L ALA* 4.1 14.7 - - - +
67L LEU* 4.3 19.1 - - + -
117L LEU* 3.3 31.3 - - + +
122L LEU* 5.0 3.1 - - + +
157L GLN* 5.4 4.8 + - - +
158L LEU* 3.6 27.6 - - + +
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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