Contacts of the helix formed by residues 16 - 22 (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 LYS 16 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C ALA* 3.9 10.3 - - + +
15C VAL* 1.3 75.0 - - - +
17C PRO* 1.4 79.0 - - + +
18C ASP* 3.1 18.4 - - - +
19C GLY 2.9 2.5 + - - -
20C VAL* 2.9 20.5 + - - +
56C TYR* 3.1 23.0 + - - -
68C LEU* 5.1 3.8 - - + +
71C PHE* 4.5 7.9 - - + -
72C ILE* 5.0 12.1 - - + -
77C VAL* 4.2 3.8 - - - -
117C GLY 6.1 0.4 - - - +
119C ASN* 2.7 30.5 + - - +
120C ILE 2.8 10.0 + - - +
121C ILE 3.7 19.7 + - - +
122C GLY* 3.8 3.1 - - - +
164C D4T 2.7 35.1 + - - -
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Residues in contact with PRO 17 (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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16C LYS* 1.4 89.8 - - + +
18C ASP* 1.3 57.3 + - - +
20C VAL* 3.9 0.5 - - - +
21C ALA* 2.8 32.3 + - - +
71C PHE* 3.3 29.6 - - + +
72C ILE* 3.6 24.0 - - - +
74C SER* 3.9 13.5 - - - +
75C GLY* 3.7 14.6 - - - +
76C PRO* 3.4 13.4 - - + +
77C VAL* 3.4 15.3 - - + -
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Residues in contact with ASP 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A ASN* 3.5 26.9 - - - +
16C LYS* 3.1 25.3 - - - +
17C PRO* 1.3 72.6 - - - +
19C GLY* 1.3 64.0 + - - +
21C ALA* 4.4 4.3 - - - -
22C ARG* 3.0 34.2 + - - +
71C PHE* 3.4 22.5 - - + -
118C ARG* 3.0 23.0 - - - +
120C ILE* 2.8 30.4 + - - +
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Residues in contact with GLY 19 (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* 3.6 17.8 - - - +
16C LYS 2.9 6.5 + - - -
18C ASP* 1.3 85.3 + - - +
20C VAL* 1.3 60.1 + - - +
22C ARG 3.6 0.3 + - - -
23C GLY 3.5 2.1 + - - -
24C LEU* 3.0 35.2 + - - +
120C ILE* 3.8 22.6 + - - -
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Residues in contact with VAL 20 (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* 3.6 20.4 - - + +
16C LYS 2.9 18.1 + - - +
17C PRO 3.9 1.3 - - - +
19C GLY* 1.3 75.0 - - - +
21C ALA* 1.3 66.8 + - - +
23C GLY* 3.0 14.9 + - - -
25C VAL* 4.0 14.5 - - + +
44C GLN* 3.8 19.3 - - - +
76C PRO* 3.5 34.3 - - + +
77C VAL* 4.0 0.4 - - - -
78C VAL* 3.9 19.5 - - + +
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Residues in contact with ALA 21 (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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152A ASN* 3.4 32.2 + - - +
17C PRO 2.8 22.8 + - - +
18C ASP 3.8 2.0 - - - +
20C VAL* 1.3 74.1 - - - +
22C ARG* 1.3 60.6 + - - +
23C GLY 3.2 1.1 + - - -
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Residues in contact with ARG 22 (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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33A GLU 5.0 0.8 + - - -
34A LYS* 3.0 20.4 + - - +
35A LYS 4.4 1.2 - - - -
36A GLY* 4.5 2.0 - - - +
150A ASN* 5.8 2.4 - - - +
152A ASN* 3.6 41.1 + - + +
153A LEU* 3.5 27.0 - - - +
18C ASP* 3.0 23.2 + - - +
19C GLY 4.1 0.4 - - - +
20C VAL 3.1 0.4 - - - -
21C ALA* 1.3 76.8 - - - +
23C GLY* 1.3 62.5 + - - +
24C LEU* 3.5 28.1 - - + +
112C PHE* 2.7 35.3 + - - +
113C GLY* 4.5 0.4 - - - -
118C ARG 5.2 1.4 + - - -
120C ILE* 3.9 18.2 - - - +
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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