Contacts of the strand formed by residues 12 - 17 (chain W) in PDB entry 3FKS
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 12 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10W THR* 3.6 29.5 - - - +
11W GLY* 1.3 77.9 - - - +
13W VAL* 1.3 65.1 + - - +
14W THR* 3.2 3.3 + - - -
23W VAL* 4.0 1.8 - - - -
24W HIS* 2.8 46.0 + - + +
73W GLY* 4.1 21.1 - - - +
74W GLU 4.2 2.7 - - - -
75W LYS* 6.1 0.9 - - - -
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Residues in contact with VAL 13 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11W GLY 3.9 0.4 + - - -
12W LYS* 1.3 72.3 - - - +
14W THR* 1.3 62.3 + - - +
15W ALA 4.2 2.9 - - - +
16W VAL* 3.6 31.2 - - + -
21W VAL* 3.9 16.8 - - + -
22W ASP 3.7 4.7 - - - +
23W VAL* 4.5 2.9 - - + +
39W ILE* 5.4 3.4 - - + -
70W LEU* 5.3 6.7 - - + -
71W VAL 4.0 6.1 - - - +
72W ARG* 3.3 11.2 - - + +
73W GLY* 3.0 30.7 + - - +
74W GLU* 3.3 33.6 + - + +
76W VAL* 3.6 14.6 - - + -
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Residues in contact with THR 14 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68S LEU 4.0 2.1 - - - +
70S PRO* 3.4 37.1 - - + +
12W LYS 3.3 1.2 + - - -
13W VAL* 1.3 74.7 - - - +
15W ALA* 1.3 59.0 + - - +
22W ASP* 2.7 21.4 + - + -
23W VAL 3.9 0.7 - - - -
24W HIS* 3.1 36.2 + - + +
58W THR* 4.6 10.1 - - + +
72W ARG* 4.1 13.3 - - - +
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Residues in contact with ALA 15 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68S LEU 3.1 12.6 - - - +
70S PRO* 3.5 26.0 - - + -
13W VAL* 3.8 1.0 - - - +
14W THR* 1.3 81.4 - - - +
16W VAL* 1.3 68.7 + - - +
17W ILE* 3.9 9.0 - - + -
20W ILE 3.8 0.3 - - - +
21W VAL* 3.4 1.7 - - - +
22W ASP* 2.7 52.1 + - + +
72W ARG* 5.2 1.1 - - - +
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Residues in contact with VAL 16 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51S ALA* 4.6 15.5 - - + -
66S LEU 3.7 5.6 - - - +
68S LEU* 2.9 45.4 + - + +
13W VAL* 3.6 22.9 - - + -
15W ALA* 1.3 79.0 - - - +
17W ILE* 1.3 65.3 + - - +
18W GLY 4.8 2.9 - - - +
20W ILE 3.5 6.5 - - - +
21W VAL* 3.8 9.2 - - + -
67W THR* 4.3 15.3 - - - +
70W LEU* 3.6 34.3 - - + -
72W ARG* 5.7 1.1 - - + -
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Residues in contact with ILE 17 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66S LEU 4.4 2.2 - - - -
67S ASN* 3.5 34.8 - - + +
68S LEU 4.8 1.1 - - - +
69S GLU* 4.7 13.7 - - + -
70S PRO* 5.5 1.3 - - + -
289S ARG* 4.0 14.1 - - + +
15W ALA* 3.9 24.2 - - + -
16W VAL* 1.3 77.0 - - - +
18W GLY* 1.3 54.1 + - - +
19W ALA 2.7 18.5 + - - -
20W ILE* 2.9 38.6 + - + +
22W ASP* 4.3 8.5 - - - +
60W ARG* 5.0 9.9 - - - +
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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
------------------------------------------------------------
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