Contacts of the strand formed by residues 67 - 72 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19F VAL* 4.0 15.3 - - + -
20F ARG 3.8 2.9 - - - -
21F LEU* 4.5 0.4 - - + +
22F LYS* 3.4 14.4 + - - -
38F MET* 4.5 4.7 - - - +
40F LEU* 4.1 11.7 - - + -
62F ILE* 3.9 25.1 - - + -
63F ARG 4.2 1.6 - - - +
64F GLY* 3.1 18.2 + - - +
66F THR* 1.3 78.9 - - - +
68F VAL* 1.3 65.6 + - - +
69F PHE* 3.5 16.2 - - - +
70F VAL* 4.0 22.0 - - + -
63G ARG* 3.4 29.7 + - + +
66G THR* 4.0 0.2 + - - -
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Residues in contact with VAL 68 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20F ARG* 2.6 35.6 + - + +
21F LEU 3.8 3.1 - - - +
22F LYS* 3.7 34.5 - - + +
67F VAL* 1.3 77.5 - - - +
69F PHE* 1.3 71.2 + - + +
21G LEU* 3.8 17.7 - - + -
62G ILE* 3.7 3.8 - - - +
63G ARG* 3.2 22.7 + - - +
66G THR* 3.7 33.2 + - + +
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Residues in contact with PHE 69 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18F ILE* 4.4 12.6 - - + -
19F VAL* 3.6 1.2 - - - -
20F ARG* 3.1 48.1 + - + -
26F GLU* 5.3 4.9 - - - -
67F VAL* 3.5 3.1 - - - +
68F VAL* 1.3 95.5 - - + +
70F VAL* 1.3 77.3 + - - +
71F SER* 4.3 15.0 - - - -
21G LEU* 5.2 0.7 - - + -
27G PHE* 3.8 34.3 - + - -
47G GLU* 4.2 21.3 - - - -
55G ARG* 5.2 13.5 - - - -
57G VAL* 6.1 0.7 - - + -
60G VAL* 4.5 8.7 - - + -
61G VAL 3.1 18.6 - - - +
62G ILE* 4.2 9.9 - - + -
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Residues in contact with VAL 70 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F LEU* 3.9 27.8 - - + -
17F VAL* 4.3 22.4 - - + -
18F ILE 3.5 8.3 - - - +
19F VAL* 4.2 9.2 - - + -
31F LEU* 5.3 2.9 - - + -
38F MET* 5.9 4.9 - - - -
40F LEU* 3.8 28.5 - - + -
67F VAL* 4.0 11.0 - - + -
69F PHE* 1.3 81.0 - - - +
71F SER* 1.3 63.8 + - - +
72F PRO* 4.6 0.2 - - - +
60G VAL* 3.6 0.5 - - - -
61G VAL* 2.8 41.4 + - + +
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Residues in contact with SER 71 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17F VAL* 3.7 4.2 - - - -
18F ILE* 3.1 40.3 + - - +
69F PHE* 4.3 11.0 - - - -
70F VAL* 1.3 72.8 - - - +
72F PRO* 1.3 70.7 + - - +
73F ALA 3.4 0.2 + - - -
55G ARG* 5.8 0.7 + - - -
57G VAL* 3.9 17.2 - - - +
59G SER 3.1 20.9 - - - -
60G VAL* 3.3 19.5 - - - -
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Residues in contact with PRO 72 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F VAL* 5.8 6.5 - - + -
12F SER* 4.3 18.4 - - - +
15F SER* 6.0 1.6 - - - +
16F PRO 4.0 8.3 - - - +
17F VAL* 4.3 4.3 - - + -
18F ILE* 5.2 0.5 - - - +
70F VAL 4.6 1.1 - - - +
71F SER* 1.3 88.3 + - - +
73F ALA* 1.3 61.3 + - - +
74F PRO* 2.8 18.6 - - + +
57G VAL* 5.5 2.8 - - - +
58G GLY* 5.5 3.0 + - - -
59G SER* 3.2 34.5 - - - +
61G VAL* 6.2 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