Contacts of the helix formed by residues 16 - 22 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ALA* 3.9 13.0 - - + +
15B VAL* 1.3 74.7 - - - +
17B PRO* 1.3 77.2 - - + +
18B ASP* 3.1 17.3 - - - +
19B GLY 2.9 12.0 + - - -
20B VAL* 3.0 10.4 + - - +
56B TYR* 3.3 15.4 + - - +
68B LEU* 4.9 2.0 - - - +
71B PHE* 4.5 4.9 - - + -
72B ILE* 4.9 13.5 - - + -
76B PRO 4.2 0.7 - - - -
77B VAL* 4.2 4.5 - - + -
117B GLY 6.2 0.2 - - - +
119B ASN* 2.7 28.9 + - - +
120B ILE 2.9 12.0 + - - +
121B ILE 3.6 19.4 + - - +
122B GLY* 3.7 2.9 - - - +
161B D4T 2.6 44.6 + - - -
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Residues in contact with PRO 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B LYS* 1.3 88.1 - - + +
18B ASP* 1.3 56.5 + - - +
20B VAL* 3.5 1.0 + - - +
21B ALA* 2.9 30.5 + - - +
71B PHE* 3.5 31.9 - - + +
72B ILE* 3.6 20.9 - - + +
74B SER* 3.9 14.1 - - - +
75B GLY* 3.6 22.4 - - - +
76B PRO 3.3 12.8 - - - +
77B VAL* 3.5 11.2 - - + -
152C ASN* 5.5 0.2 - - - -
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Residues in contact with ASP 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B LYS* 3.3 21.8 - - - +
17B PRO* 1.3 71.8 - - - +
19B GLY* 1.3 67.7 + - - +
21B ALA* 3.8 1.0 - - - -
22B ARG* 2.9 34.3 + - - +
71B PHE* 3.5 20.2 - - + -
118B ARG* 3.0 26.5 - - - +
120B ILE* 2.9 30.8 + - - +
152C ASN* 3.4 31.8 - - + +
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Residues in contact with GLY 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B VAL* 3.6 16.8 - - - -
16B LYS 2.9 7.7 + - - -
18B ASP* 1.3 84.7 + - - +
20B VAL* 1.3 58.3 + - - +
22B ARG 3.4 0.3 + - - -
23B GLY 3.3 3.6 + - - -
24B LEU* 3.0 36.1 + - - +
25B VAL 4.1 0.2 + - - -
120B ILE* 3.8 21.0 + - - -
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Residues in contact with VAL 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B VAL* 3.5 20.4 - - + +
16B LYS 3.0 10.1 + - - +
17B PRO 3.8 2.9 - - - +
19B GLY* 1.3 77.4 - - - +
21B ALA* 1.3 62.7 + - - +
23B GLY* 3.0 14.4 + - - -
25B VAL* 4.0 19.5 - - + +
44B GLN* 3.7 21.1 - - - +
76B PRO* 3.4 39.3 - - + +
77B VAL* 4.0 0.2 - - - -
78B VAL* 3.9 12.8 - - + +
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Residues in contact with ALA 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B PRO 2.9 18.6 + - - +
18B ASP 3.8 0.9 - - - +
20B VAL* 1.3 79.2 - - - +
22B ARG* 1.3 61.0 + - - +
23B GLY 3.2 1.1 + - - -
150C ASN* 5.5 1.0 + - - -
152C ASN* 3.4 34.6 + - - +
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Residues in contact with ARG 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B ASP* 2.9 23.9 + - - +
19B GLY 4.0 3.4 - - - +
20B VAL 3.1 0.4 - - - -
21B ALA* 1.3 77.1 - - - +
23B GLY* 1.3 63.1 + - - +
24B LEU* 3.4 23.9 + - + +
112B PHE* 2.8 33.1 + - - +
113B GLY* 4.5 1.2 - - - -
118B ARG 5.3 1.2 + - - -
120B ILE* 3.8 21.4 - - - +
33C GLU 5.0 0.6 + - - -
34C LYS 3.0 20.2 + - - -
35C LYS 4.3 1.2 - - - -
36C GLY* 4.4 2.2 - - - +
150C ASN* 4.0 19.3 - - - +
152C ASN* 3.6 35.8 + - + +
153C LEU* 3.4 25.2 - - - +
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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