Contacts of the strand formed by residues 67 - 72 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19I VAL* 4.3 1.1 - - + -
20I ARG 3.9 4.9 - - - +
21I LEU* 4.0 6.7 - - + -
22I LYS* 5.1 1.8 - - - +
38I MET* 4.6 6.3 - - - +
40I LEU* 4.0 17.7 - - + -
62I ILE* 3.9 25.8 - - + -
63I ARG 4.0 3.1 - - - +
64I GLY* 3.0 20.2 + - - +
65I ASP 4.3 2.9 - - - +
66I THR* 1.3 79.8 - - - +
68I VAL* 1.3 64.5 + - - +
69I PHE* 3.6 22.4 - - - +
70I VAL* 4.0 15.0 - - + -
63J ARG* 3.5 30.7 + - + +
66J THR* 3.9 4.3 + - - -
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Residues in contact with VAL 68 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20I ARG* 3.2 17.2 + - + +
21I LEU 3.7 5.8 - - - +
22I LYS* 3.6 41.3 - - + +
67I VAL* 1.3 77.0 - - - +
69I PHE* 1.3 74.2 + - + +
21J LEU* 3.8 15.5 - - + -
25J ARG* 6.3 0.2 - - - +
62J ILE* 3.7 4.0 - - - +
63J ARG* 3.0 24.8 + - - +
66J THR* 3.6 30.1 + - + +
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Residues in contact with PHE 69 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18I ILE* 4.7 7.6 - - + -
19I VAL* 3.7 0.9 - - - -
20I ARG* 3.0 61.1 + - + +
26I GLU* 5.0 0.2 - - - -
67I VAL* 3.6 3.9 - - - +
68I VAL* 1.3 93.3 - - + +
70I VAL* 1.3 80.4 + - - +
71I SER* 4.1 17.5 - - - -
21J LEU* 5.3 1.6 - - + -
25J ARG* 4.9 2.9 - - - -
27J PHE* 3.5 35.7 - + - -
47J GLU* 4.2 7.6 - - - -
55J ARG* 4.1 22.7 - - - -
57J VAL* 5.9 2.9 - - + -
60J VAL* 4.1 10.8 - - + -
61J VAL 3.3 13.0 - - - +
62J ILE* 4.2 12.6 - - + -
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Residues in contact with VAL 70 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9I LEU* 3.8 30.3 - - + -
17I VAL* 4.5 16.6 - - + -
18I ILE 3.5 7.6 - - - +
19I VAL* 4.1 12.3 - - + -
31I LEU* 5.4 3.1 - - + -
38I MET* 5.3 6.3 - - - -
40I LEU* 3.8 28.0 - - + -
67I VAL* 4.0 10.5 - - + -
69I PHE* 1.3 81.7 - - - +
71I SER* 1.3 65.5 + - - +
72I PRO* 4.4 1.5 - - + +
60J VAL* 3.4 2.8 - - - -
61J VAL* 3.0 38.3 + - + +
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Residues in contact with SER 71 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17I VAL* 3.3 4.8 - - - -
18I ILE* 2.6 49.1 + - - +
69I PHE* 4.1 10.1 - - - -
70I VAL* 1.3 78.6 - - - +
72I PRO* 1.3 67.1 + - - +
57J VAL* 3.1 27.4 - - - +
59J SER 2.6 20.6 + - - -
60J VAL* 3.5 12.5 - - - +
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Residues in contact with PRO 72 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8I VAL* 6.2 3.6 - - + -
12I SER* 4.6 17.5 - - - +
15I SER* 5.2 2.2 - - - +
16I PRO 3.8 10.8 - - - +
17I VAL* 4.1 6.2 - - + -
18I ILE* 5.8 0.2 - - - +
70I VAL* 4.4 2.5 - - + +
71I SER* 1.3 90.3 + - - +
73I ALA* 1.3 58.4 + - - +
57J VAL* 4.9 6.1 - - - +
58J GLY* 5.5 4.6 + - - -
59J SER* 3.1 37.7 - - - +
60J VAL* 5.1 0.2 - - - -
61J VAL* 6.3 1.6 - - + -
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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