Contacts of the strand formed by residues 12 - 17 (chain X) 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 X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11X GLY* 1.3 77.2 - - - +
13X VAL* 1.3 65.4 + - - +
14X THR* 3.4 6.1 + - + +
23X VAL* 3.4 5.0 - - - +
24X HIS* 2.8 49.2 + - + +
26X GLU* 4.2 17.3 - - - +
73X GLY* 3.2 35.5 + - - +
74X GLU 3.6 0.7 - - - -
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Residues in contact with VAL 13 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12X LYS* 1.3 70.4 - - - +
14X THR* 1.3 63.3 + - - +
15X ALA 4.5 0.9 - - - +
16X VAL* 3.9 27.4 - - + -
21X VAL* 4.4 9.0 - - + -
22X ASP 3.6 8.7 - - - +
23X VAL* 4.6 5.8 - - + +
39X ILE* 4.6 8.5 - - + -
70X LEU* 5.6 7.4 - - + -
71X VAL 3.9 11.7 - - - +
72X ARG* 3.2 11.1 - - - +
73X GLY* 2.6 34.9 + - - +
74X GLU* 3.4 31.0 + - + +
76X VAL* 4.1 13.5 - - + -
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Residues in contact with THR 14 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70T PRO* 4.0 24.1 - - + +
12X LYS* 3.7 17.0 - - + +
13X VAL* 1.3 75.5 - - - +
15X ALA* 1.3 70.5 + - - +
22X ASP* 3.0 25.1 + - - +
24X HIS* 3.9 20.6 - - + +
58X THR* 4.2 9.1 - - + +
72X ARG* 3.2 27.0 - - - +
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Residues in contact with ALA 15 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68T LEU 3.0 12.3 - - - +
69T GLU* 4.4 0.9 - - + -
70T PRO* 3.7 17.0 - - + -
13X VAL* 4.7 0.2 - - - +
14X THR* 1.3 83.6 + - - +
16X VAL* 1.3 68.2 + - - +
17X ILE* 4.1 10.3 - - + -
20X ILE 3.8 0.7 - - - +
21X VAL* 3.6 1.4 - - - +
22X ASP* 2.8 52.7 + - + +
72X ARG* 4.9 0.2 - - - -
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Residues in contact with VAL 16 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51T ALA* 4.6 4.7 - - + -
66T LEU 4.0 1.3 - - - +
67T ASN* 3.7 2.6 - - - -
68T LEU* 2.9 52.6 + - + +
13X VAL* 3.9 21.5 - - + -
15X ALA* 1.3 78.6 - - - +
17X ILE* 1.3 63.0 + - - +
18X GLY 4.0 2.5 + - - +
20X ILE 3.6 5.4 - - - +
21X VAL* 4.6 6.1 - - + -
67X THR* 3.9 35.9 - - + +
70X LEU* 4.2 26.5 - - + +
72X ARG* 5.2 1.8 - - + -
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Residues in contact with ILE 17 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67T ASN* 3.4 32.3 - - + -
68T LEU 3.9 13.9 - - - +
69T GLU* 4.1 15.5 - - + +
289T ARG* 5.8 2.7 - - - +
15X ALA* 4.8 8.1 - - + -
16X VAL* 1.3 76.9 - - - +
18X GLY* 1.3 57.7 + - - +
19X ALA 2.8 0.7 + - - -
20X ILE* 2.8 48.2 + - + +
22X ASP* 5.6 2.5 - - - +
60X ARG* 6.3 0.9 - - - +
271X LEU* 3.6 32.2 - - + +
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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