Contacts of the helix formed by residues 24 - 36 (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 LEU 24 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C VAL* 5.0 0.2 - - - -
19C GLY* 3.0 16.2 + - - +
22C ARG* 4.0 46.4 - - + +
23C GLY* 1.3 81.3 - - - +
25C VAL* 1.3 65.0 + - - +
26C GLY 3.4 2.2 - - - -
27C GLU* 3.4 11.3 + - + +
28C ILE* 3.0 38.0 + - + +
112C PHE* 4.0 41.7 - - + -
120C ILE* 4.1 17.9 - - + -
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Residues in contact with VAL 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C VAL* 4.2 8.5 - - + +
19C GLY 4.1 0.2 + - - -
20C VAL* 4.0 31.2 - - + +
23C GLY* 3.6 2.5 - - - -
24C LEU* 1.3 79.5 - - - +
26C GLY* 1.3 60.6 + - - +
28C ILE* 3.6 1.4 - - - +
29C ILE* 2.9 49.6 + - + +
42C LEU* 6.0 0.2 - - + -
78C VAL* 3.8 40.4 - - + -
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Residues in contact with GLY 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C GLY 5.2 1.2 + - - -
24C LEU 3.4 0.2 - - - -
25C VAL* 1.3 78.0 - - - +
27C GLU* 1.3 60.2 + - - +
29C ILE* 3.9 6.9 - - - +
30C ALA* 2.8 32.5 + - - +
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Residues in contact with GLU 27 (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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34A LYS* 6.0 2.2 - - - -
23C GLY 5.3 2.1 + - - +
24C LEU* 3.4 20.5 + - + +
25C VAL 3.3 0.4 - - - -
26C GLY* 1.3 75.5 - - - +
28C ILE* 1.3 64.1 + - + +
30C ALA* 3.4 6.7 + - - +
31C ARG* 2.9 56.8 + - - +
112C PHE* 3.6 30.8 - - + -
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Residues in contact with ILE 28 (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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15C VAL* 3.9 30.7 - - + -
24C LEU* 3.0 25.9 + - + +
25C VAL 3.6 2.9 - - - +
27C GLU* 1.3 78.6 - - + +
29C ILE* 1.3 69.4 + - - +
31C ARG* 3.1 17.2 + - - +
32C TYR* 3.3 24.2 - - + -
80C MET* 4.8 5.8 - - + -
108C ILE* 4.1 20.9 - - + -
112C PHE* 5.5 1.1 - - + -
120C ILE* 3.6 30.5 - - + -
121C ILE* 3.7 26.7 - - + -
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Residues in contact with ILE 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C VAL* 5.8 0.2 - - + -
25C VAL* 2.9 38.7 + - + +
26C GLY* 3.9 6.1 - - - +
28C ILE* 1.3 75.9 - - + +
30C ALA* 1.3 63.8 + - - +
32C TYR* 3.1 6.6 + - - +
33C GLU* 2.9 42.6 + - + +
39C LEU* 4.7 10.1 - - + -
42C LEU* 4.1 28.3 - - + -
80C MET* 3.6 21.5 - - - -
82C PHE* 4.4 14.4 - - + -
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Residues in contact with ALA 30 (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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26C GLY 2.8 19.3 + - - +
27C GLU* 3.6 8.5 - - - +
29C ILE* 1.3 79.2 - - - +
31C ARG* 1.3 57.0 + - - +
33C GLU* 3.2 13.9 + - - +
34C LYS* 2.9 51.9 + - - +
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Residues in contact with ARG 31 (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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111B ASP 4.5 1.6 - - - +
27C GLU* 2.9 39.7 + - - +
28C ILE* 3.1 8.8 + - - +
30C ALA* 1.3 77.5 - - - +
32C TYR* 1.3 62.3 + - + +
34C LYS* 3.5 11.6 + - + +
35C LYS* 3.3 16.8 + - - +
94C MET* 3.5 23.8 + - + +
106C GLY 2.9 28.5 + - - -
107C SER 3.6 11.5 - - - -
108C ILE* 3.5 23.9 - - + +
111C ASP* 2.7 22.8 + - - -
112C PHE* 3.4 22.9 - - - -
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Residues in contact with TYR 32 (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* 3.5 24.5 - - + +
28C ILE* 3.3 28.9 + - + -
29C ILE 3.1 2.2 + - - +
31C ARG* 1.3 74.0 - - - +
33C GLU* 1.3 65.5 + - - +
35C LYS* 3.4 7.8 + - - +
37C PHE* 3.2 37.5 + + + +
82C PHE* 3.4 36.1 - + + -
87C VAL* 5.8 0.2 - - + -
91C ALA* 3.1 46.4 + - + +
94C MET* 3.5 27.5 - - + +
95C ILE* 3.3 18.4 - - - +
108C ILE* 3.7 25.0 - - + +
121C ILE* 4.0 1.3 - - + +
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Residues in contact with GLU 33 (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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22B ARG* 5.0 0.9 + - - -
29C ILE* 2.9 38.7 + - + +
30C ALA* 3.6 15.9 - - - +
32C TYR* 1.3 76.0 - - - +
34C LYS* 1.3 57.6 + - + +
36C GLY* 2.9 22.0 + - - -
37C PHE 4.0 10.0 - - - +
39C LEU* 5.7 5.8 - - + +
82C PHE* 4.7 8.1 - - + -
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Residues in contact with LYS 34 (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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22B ARG* 3.0 24.8 + - - -
111B ASP* 3.6 6.5 - - + +
112B PHE* 3.4 40.2 - - + -
30C ALA* 2.9 37.2 + - - +
31C ARG* 3.7 10.1 - - + +
33C GLU* 1.3 77.5 - - + +
35C LYS* 1.3 56.7 + - - +
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Residues in contact with LYS 35 (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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100B PRO 3.0 23.0 + - - -
101B LEU* 4.3 3.9 + - - +
103B SER 4.6 2.2 + - - -
109B ARG 3.4 3.0 + - - -
110B GLY* 2.8 30.4 + - - +
111B ASP 3.2 13.2 + - - +
112B PHE* 3.1 15.5 - - - +
113B GLY 2.9 27.3 + - - +
114B VAL* 3.4 17.4 - - + +
31C ARG 3.3 11.2 + - - +
32C TYR 3.4 11.2 - - - +
34C LYS* 1.3 78.4 - - - +
36C GLY* 1.3 57.6 + - - +
37C PHE* 3.4 26.9 - - + -
90C SER* 3.4 21.9 + - - -
94C MET* 3.9 14.1 - - + -
153C LEU* 3.9 1.2 - - - +
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Residues in contact with GLY 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ARG* 4.4 1.8 - - - -
114B VAL* 4.9 2.5 - - - -
33C GLU 2.9 13.1 + - - -
34C LYS 3.1 1.5 - - - -
35C LYS* 1.3 79.6 - - - +
37C PHE* 1.3 68.9 + - - +
38C VAL* 3.6 9.4 + - - +
83C GLU 4.8 0.7 - - - +
149C PRO* 5.3 0.9 - - - +
153C LEU* 3.1 39.3 - - - +
154C TYR* 4.9 4.0 + - - -
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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