Contacts of the strand formed by residues 16 - 21 (chain J) 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 J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15J SER* 1.3 88.9 + - - +
17J VAL* 1.3 70.8 + - - +
28J ARG* 6.4 1.8 - - + -
29J GLY 3.4 12.6 - - - +
30J THR* 4.3 3.4 - - - +
72J PRO* 3.9 3.1 - - - +
73J ALA* 3.3 34.2 + - + +
74J PRO* 5.4 2.2 - - + -
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Residues in contact with VAL 17 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12J SER* 4.3 17.5 - - - -
15J SER* 4.1 2.7 - - - +
16J PRO* 1.3 82.7 - - - +
18J ILE* 1.3 65.5 + - - +
19J VAL* 4.3 5.5 - - + +
27J PHE 4.7 0.2 - - - -
28J ARG* 3.5 6.4 - - - +
29J GLY 2.8 37.0 + - - +
31J LEU* 4.0 26.2 - - + -
42J LEU* 3.9 22.2 - - + -
70J VAL* 4.1 20.0 - - + -
71J SER 3.4 9.6 - - - +
72J PRO* 4.2 9.9 - - + -
73J ALA* 3.9 2.5 - - - +
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Residues in contact with ILE 18 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17J VAL* 1.3 75.3 - - - +
19J VAL* 1.3 73.6 + - - +
26J GLU* 4.9 9.9 - - + +
27J PHE 3.5 9.0 - - - +
28J ARG* 4.1 31.4 - - + +
48J ILE* 5.9 2.2 - - + -
69J PHE* 3.9 12.3 - - + +
70J VAL* 3.2 5.7 - - - +
71J SER* 2.7 41.8 + - - +
73J ALA* 3.3 28.0 - - + -
55K ARG* 4.5 24.9 - - - +
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Residues in contact with VAL 19 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17J VAL* 4.3 13.5 - - + -
18J ILE* 1.3 83.9 - - - +
20J ARG* 1.3 63.4 + - - +
21J LEU* 3.7 24.9 - - + +
26J GLU* 3.1 7.3 - - - +
27J PHE* 2.9 37.2 + - + +
40J LEU* 4.1 29.6 - - + -
42J LEU* 4.1 24.2 - - + -
62J ILE* 4.5 6.5 - - + -
67J VAL* 4.3 4.3 - - + -
69J PHE 3.4 8.7 - - - +
70J VAL* 4.3 4.7 - - + -
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Residues in contact with ARG 20 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19J VAL* 1.3 74.4 - - - +
21J LEU* 1.3 75.8 + - - +
23J GLY 5.0 0.8 - - - +
24J GLY* 3.3 36.3 + - - +
25J ARG 3.7 3.4 - - - +
26J GLU* 3.5 26.7 + - + +
67J VAL* 3.9 0.9 - - - +
68J VAL* 3.1 34.4 + - + +
69J PHE* 3.0 53.8 + - + +
25K ARG* 3.5 37.5 - - - +
47K GLU* 4.0 10.0 + - - -
55K ARG* 4.4 2.0 - - - +
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Residues in contact with LEU 21 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68I VAL* 3.8 17.0 - - + -
69I PHE* 5.3 1.3 - - + -
19J VAL* 3.7 20.6 - - + +
20J ARG* 1.3 89.9 + - - +
22J LYS* 1.3 57.2 + - - +
23J GLY 2.7 16.9 + - - -
24J GLY* 3.1 11.6 + - - -
25J ARG* 2.9 28.4 + - + +
27J PHE* 4.6 22.7 - - + -
62J ILE* 4.1 17.9 - - + -
66J THR* 3.4 35.4 - - + +
67J VAL* 4.1 4.5 - - - -
68J VAL* 3.7 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