Contacts of the strand formed by residues 16 - 21 (chain C) 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 PRO 16 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C LYS 4.7 0.9 - - - +
15C SER* 1.3 92.2 + - - +
17C VAL* 1.3 65.7 + - - +
29C GLY 3.4 11.9 - - - +
30C THR* 4.4 3.5 - - - +
72C PRO* 3.7 3.5 - - - +
73C ALA* 3.3 36.3 + - + +
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Residues in contact with VAL 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C SER* 4.4 10.1 - - - -
15C SER* 3.8 13.2 - - - +
16C PRO* 1.3 80.5 - - - +
18C ILE* 1.3 65.9 + - - +
19C VAL* 4.3 9.0 - - + -
27C PHE 3.6 0.9 - - - +
28C ARG* 3.4 6.8 + - - +
29C GLY 2.9 35.3 + - - +
31C LEU* 4.0 20.4 - - + -
42C LEU* 3.9 23.3 - - + -
70C VAL* 4.3 15.5 - - + -
71C SER 3.4 13.7 - - - +
72C PRO* 4.1 7.4 - - + -
73C ALA* 4.0 2.8 - - - +
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Residues in contact with ILE 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C VAL* 1.3 75.5 - - - +
19C VAL* 1.3 63.3 + - - +
20C ARG 4.1 0.2 + - - -
26C GLU* 3.7 21.1 - - - +
27C PHE 3.4 5.6 - - - +
28C ARG* 3.3 32.3 - - + +
69C PHE* 3.8 7.1 - - + +
70C VAL* 3.4 4.5 - - - +
71C SER* 2.7 43.0 + - - +
73C ALA* 3.3 25.4 - - + -
55D ARG* 3.4 31.6 - - - +
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Residues in contact with VAL 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C VAL* 4.3 14.8 - - + -
18C ILE* 1.3 77.0 - - - +
20C ARG* 1.3 61.3 + - - +
21C LEU* 3.7 20.4 + - + +
26C GLU* 3.1 10.1 - - - +
27C PHE* 2.7 50.1 + - + +
40C LEU* 4.0 28.9 - - + -
42C LEU* 3.9 22.7 - - + -
62C ILE* 4.3 5.4 - - + -
67C VAL* 4.3 8.3 - - + -
69C PHE 3.7 2.7 - - - +
70C VAL* 4.2 10.8 - - + -
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Residues in contact with ARG 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C ILE 4.1 0.6 + - - -
19C VAL* 1.3 72.4 - - - +
21C LEU* 1.3 67.8 + - - +
24C GLY* 3.3 25.6 + - - -
25C ARG 4.2 4.9 - - - -
26C GLU* 3.7 23.3 + - + -
67C VAL* 3.8 1.0 - - - +
68C VAL* 2.8 44.8 + - + +
69C PHE* 2.9 45.5 + - + +
25D ARG* 2.8 38.6 - - - +
47D GLU* 3.9 17.9 + - - -
49D GLN* 5.5 6.3 + - - +
55D ARG* 5.5 1.5 - - - +
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Residues in contact with LEU 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B ARG* 5.9 1.3 - - - +
68B VAL* 3.9 24.0 - - + -
69B PHE* 5.0 1.6 - - + -
19C VAL* 3.7 14.8 + - + +
20C ARG* 1.3 85.2 + - - +
22C LYS* 1.3 69.1 + - - +
23C GLY 3.6 1.6 + - - -
24C GLY 3.7 8.5 + - - -
25C ARG* 3.3 35.0 + - + +
27C PHE* 3.9 31.4 - - + -
47C GLU* 5.6 0.7 - - - +
62C ILE* 3.9 25.1 - - + -
66C THR* 3.3 23.1 - - + +
67C VAL* 4.6 2.2 - - + -
68C VAL* 3.7 5.2 - - - +
25D ARG* 4.5 1.2 + - - -
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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