Contacts of the strand formed by residues 67 - 72 (chain D) in PDB entry 1I5L
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 67 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D VAL* 3.9 6.7 - - + -
20D ARG 3.6 8.3 - - - +
21D LEU* 4.0 4.9 - - + -
22D LYS* 4.6 5.4 - - - -
38D MET* 4.7 5.8 - - + +
40D LEU* 4.1 10.8 - - + -
62D ILE* 3.8 26.7 - - + -
63D ARG 3.8 4.9 - - - +
64D GLY* 2.9 15.8 + - - +
66D THR* 1.3 79.1 - - - +
68D VAL* 1.3 63.9 + - - +
69D PHE* 3.3 29.6 - - - +
70D VAL* 3.9 12.1 - - + -
63E ARG* 3.7 28.7 + - + +
66E THR* 4.2 3.5 + - - -
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Residues in contact with VAL 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D ARG* 3.3 19.9 + - + +
21D LEU 3.7 6.5 - - - +
22D LYS* 3.7 37.5 - - + +
67D VAL* 1.3 77.6 - - - +
69D PHE* 1.3 79.2 + - + +
21E LEU* 4.4 12.6 - - + -
62E ILE* 3.6 6.2 - - - +
63E ARG* 3.3 20.5 + - - +
66E THR* 3.9 30.3 + - + +
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Residues in contact with PHE 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D ILE* 4.6 7.6 - - + -
20D ARG* 2.9 66.8 + - + -
26D GLU* 5.9 0.4 - - - -
67D VAL* 3.3 5.7 - - - +
68D VAL* 1.3 95.4 - - + +
70D VAL* 1.3 79.8 + - - +
71D SER* 4.3 15.5 - - - -
21E LEU* 6.1 0.4 - - + -
27E PHE* 3.9 30.5 - + - -
47E GLU* 4.2 19.7 - - - -
55E ARG* 4.8 17.3 - - - -
57E VAL* 5.7 0.9 - - + -
60E VAL* 4.2 10.5 - - + -
61E VAL 3.2 16.4 - - - +
62E ILE* 4.2 10.5 - - + -
63E ARG* 4.9 0.7 - - - +
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Residues in contact with VAL 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D LEU* 4.1 28.0 - - + -
17D VAL* 4.1 26.7 - - + -
18D ILE 3.5 8.1 - - - +
19D VAL* 4.4 4.7 - - + -
31D LEU* 5.3 1.6 - - + -
38D MET* 5.8 4.7 - - - -
40D LEU* 3.8 28.7 - - + -
67D VAL* 3.9 9.9 - - + -
69D PHE* 1.3 82.4 - - - +
71D SER* 1.3 63.8 + - - +
72D PRO* 4.3 2.6 - - + +
60E VAL* 3.6 2.8 - - - -
61E VAL* 3.0 38.5 + - + +
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Residues in contact with SER 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D VAL* 3.5 4.1 - - - -
18D ILE* 2.9 40.2 + - - +
69D PHE* 4.3 11.4 - - - -
70D VAL* 1.3 78.1 - - - +
72D PRO* 1.3 78.4 + - - +
55E ARG* 6.0 0.9 - - - -
57E VAL* 3.7 20.5 - - - +
59E SER 3.0 18.9 + - - -
60E VAL* 3.9 11.7 - - - -
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Residues in contact with PRO 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D VAL* 5.6 7.6 - - + -
12D SER* 4.1 21.5 - - - +
15D SER* 5.8 2.0 - - - +
16D PRO 3.9 8.7 - - - +
17D VAL* 4.5 4.7 - - + -
18D ILE* 5.5 0.5 - - - +
70D VAL* 4.3 4.0 - - + +
71D SER* 1.3 92.3 + - - +
73D ALA* 1.3 67.5 + - - +
58E GLY* 5.5 4.0 + - - -
59E SER* 3.5 32.1 - - - +
60E VAL* 5.2 0.4 - - - -
61E VAL* 6.5 0.4 - - + -
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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