Contacts of the strand formed by residues 10 - 15 (chain C) in PDB entry 1F3F
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 ARG 10 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8C LYS* 3.5 12.5 + - - +
9C GLU* 1.3 81.1 - - - +
11C THR* 1.3 60.8 + - - +
40C VAL* 3.8 17.1 - - - +
81C VAL* 4.0 6.3 - - + -
82C PHE 3.2 7.9 - - - +
83C GLU* 2.8 32.4 + - + +
87C VAL* 3.6 3.4 - - - -
88C VAL* 3.2 16.6 - - - +
127C VAL* 5.3 1.4 - - - +
130C ALA* 3.4 9.5 - - - +
131C ASN* 4.9 6.5 + - - +
134C ILE* 3.7 19.2 - - + +
143C LEU* 3.8 33.3 - - - +
144C LEU 2.8 25.2 + - - -
145C THR* 4.8 1.6 + - - +
147C VAL* 4.0 8.1 - - - +
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Residues in contact with THR 11 (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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10C ARG* 1.3 77.4 - - - +
12C PHE* 1.3 64.6 + - - +
13C LEU* 4.1 14.3 + - + +
81C VAL* 3.3 8.0 - - - +
82C PHE* 3.0 34.5 + - + +
87C VAL* 3.6 31.0 - - + +
88C VAL* 3.5 21.3 + - - +
91C ALA* 4.1 11.6 - - + +
124C SER* 3.3 25.1 + - - -
130C ALA* 3.9 5.2 - - - -
134C ILE* 4.1 4.9 - - - -
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Residues in contact with PHE 12 (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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11C THR* 1.3 76.2 + - - +
13C LEU* 1.3 67.8 + - - +
14C ALA* 3.7 29.6 - - + -
55C HIS* 3.5 33.9 - + - -
79C ALA* 3.7 17.7 - - + -
80C MET 3.4 11.9 - - - -
81C VAL* 4.4 4.0 - - + -
122C GLY 5.2 1.3 - - - -
123C GLY* 3.2 4.4 - - - -
124C SER* 3.0 38.8 + - - +
133C GLU* 3.7 17.5 - - + +
134C ILE* 3.9 17.3 - - + +
137C TRP* 3.3 46.0 - + + -
138C PHE* 4.0 7.6 - + - -
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Residues in contact with LEU 13 (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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11C THR* 4.1 13.5 - - + +
12C PHE* 1.3 86.4 - - - +
14C ALA* 1.3 59.6 + - - +
15C VAL* 4.2 0.7 - - + -
32C TYR* 3.5 38.1 - - + -
79C ALA* 3.6 1.0 - - - -
80C MET* 2.7 53.7 + - + +
82C PHE* 3.7 24.7 - - + -
91C ALA* 3.8 22.9 - - + -
95C ILE* 4.1 8.5 - - + -
121C ILE* 4.4 7.4 - - + -
122C GLY 3.1 6.7 - - - +
123C GLY* 3.5 17.9 - - - -
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Residues in contact with ALA 14 (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 PHE* 3.7 23.7 - - + -
13C LEU* 1.3 76.0 - - - +
15C VAL* 1.3 64.5 + - - +
16C LYS* 3.2 8.3 + - + +
55C HIS* 5.6 2.0 - - - +
72C ILE* 5.3 4.0 - - + -
77C VAL* 3.9 19.1 - - + -
78C VAL 3.3 3.8 - - - -
79C ALA* 4.7 0.2 - - - -
121C ILE* 3.2 5.4 - - - -
122C GLY* 2.9 35.8 + - - +
137C TRP* 4.8 5.6 - - + -
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Residues in contact with VAL 15 (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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13C LEU 4.2 0.2 - - - -
14C ALA* 1.3 72.0 - - - +
16C LYS* 1.3 64.5 + - - +
19C GLY* 3.6 35.0 - - - +
20C VAL* 3.6 6.6 - - + +
25C VAL* 4.2 10.5 - - + -
28C ILE* 3.9 40.4 - - + -
77C VAL* 3.2 6.1 - - - +
78C VAL* 2.7 54.4 + - + +
80C MET* 4.4 8.5 - - - -
120C ILE 3.6 5.4 - - - +
121C ILE* 4.4 4.3 - - + +
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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