Contacts of the strand formed by residues 15 - 22 (chain F) in PDB entry 4NAW
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 15 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12F TRP* 4.1 4.4 + - - -
13F PHE* 3.4 41.6 + - - +
14F GLY* 1.3 86.3 + - - -
16F ILE* 1.3 65.3 + - - +
17F PRO* 4.0 6.2 - - - +
38F LEU* 3.8 44.5 + - + +
39F LEU 3.3 12.1 - - - -
40F PRO* 3.4 24.4 - - - +
41F ARG* 4.3 5.8 + - - +
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Residues in contact with ILE 16 (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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15F ARG* 1.3 77.4 - - - +
17F PRO* 1.3 79.3 - - + +
18F THR* 3.0 12.7 + - - +
38F LEU* 4.3 1.3 - - - -
39F LEU* 2.8 39.5 + - + +
41F ARG* 3.7 33.2 - - + +
83F ILE* 4.2 11.9 - - + -
84F GLY* 3.9 10.3 - - - -
87F PHE* 3.4 51.1 - - + -
96F LEU* 4.6 0.2 - - + -
98F TRP* 3.9 14.8 - - + -
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Residues in contact with PRO 17 (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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15F ARG 4.0 6.5 - - - +
16F ILE* 1.3 86.9 - - + +
18F THR* 1.3 59.3 + - - +
37F LEU 3.8 4.7 - - - +
38F LEU* 3.8 20.4 - - + -
96F LEU* 4.0 34.0 - - + +
97F PRO* 3.4 11.8 - - + +
98F TRP* 2.9 22.9 + - - +
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Residues in contact with THR 18 (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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16F ILE 3.0 13.7 + - - -
17F PRO* 1.3 73.7 + - - +
19F CYS* 1.3 63.0 + - - +
20F PHE* 3.6 25.3 - - + -
35F TYR 3.8 1.0 - - - +
36F TYR* 3.3 8.0 - - - -
37F LEU 2.8 40.7 + - - -
39F LEU* 3.4 17.6 - - + +
97F PRO* 4.2 3.8 - - - +
98F TRP* 3.3 23.6 - - + +
100F ILE* 3.7 25.4 - - + -
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Residues in contact with CYS 19 (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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34C GLU* 5.5 3.6 - - - -
18F THR* 1.3 71.4 - - - +
20F PHE* 1.3 59.9 - - - +
21F THR* 3.7 18.5 + - - -
34F PRO* 4.1 12.3 - - - -
35F TYR 3.9 2.7 - - - -
36F TYR* 3.5 39.3 - - + -
97F PRO* 4.0 7.3 - - + +
98F TRP 2.8 9.6 + - - +
99F ASN* 3.7 24.2 + - - +
100F ILE 3.0 25.9 + - - +
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Residues in contact with PHE 20 (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 THR* 3.6 27.6 - - + -
19F CYS* 1.3 71.6 - - - +
21F THR* 1.3 59.7 + - - +
34F PRO* 3.4 4.0 - - - +
35F TYR* 2.8 46.9 + - + +
37F LEU* 4.1 13.5 - - + -
39F LEU* 3.9 18.6 - - + -
45F LEU* 4.6 2.0 - - + -
49F THR* 4.0 17.3 - - + -
52F VAL* 3.8 24.9 - - + -
56F PHE* 3.3 23.9 - - + -
70F PHE* 3.8 18.8 - + - -
100F ILE* 3.4 31.6 - - + -
102F VAL* 3.9 12.6 - - + -
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Residues in contact with THR 21 (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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19F CYS* 3.7 19.4 + - - -
20F PHE* 1.3 74.6 + - - +
22F LEU* 1.3 74.2 + - - +
34F PRO* 4.3 13.8 - - + +
56F PHE* 4.3 2.5 - - - -
99F ASN* 5.1 2.6 + - - -
100F ILE 3.0 9.9 + - - -
101F THR* 3.3 10.0 - - + +
102F VAL 2.8 24.8 + - - -
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Residues in contact with LEU 22 (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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21F THR* 1.3 84.3 - - - +
23F TYR* 1.3 74.4 + - - +
24F GLN* 3.3 4.2 + - - +
26F GLU* 4.1 11.0 - - + -
28F THR* 3.8 29.6 - - + -
32F ALA* 4.2 16.0 + - + +
56F PHE* 3.7 25.5 - - + +
59F VAL* 4.0 17.7 - - + -
60F MET* 4.7 2.9 - - - -
101F THR* 4.5 0.2 - - - -
102F VAL* 3.6 26.0 - - + +
104F PHE* 3.9 26.0 - - + -
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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