Contacts of the strand formed by residues 26 - 33 (chain F) in PDB entry 3STJ
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 VAL 26 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22F VAL 4.5 7.2 - - - +
23F LEU* 3.0 19.8 + - - +
24F PRO 3.8 4.5 - - - +
25F ALA* 1.3 79.4 - - + +
27F VAL* 1.3 64.8 + - - +
67F GLY 3.5 15.7 - - - +
68F VAL* 4.6 4.0 - - + +
95F ASN* 4.8 7.8 + - - +
127F ILE* 5.2 4.0 - - + -
144F VAL* 3.7 51.6 - - + +
145F GLY* 4.5 4.3 - - - +
152F GLN* 3.6 10.9 - - + +
189F GLY* 4.7 1.3 - - - -
190F ALA* 3.9 24.5 - - + +
192F LEU* 5.2 4.5 - - + -
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Residues in contact with VAL 27 (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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24F PRO 4.4 0.9 - - - +
26F VAL* 1.3 81.5 - - - +
28F SER* 1.3 57.2 + - - +
29F VAL* 4.3 1.3 - - + -
66F SER* 3.3 8.5 - - - -
67F GLY* 2.8 51.4 + - - +
68F VAL 4.4 0.2 - - - +
69F ILE* 3.6 24.0 - - + -
77F VAL* 3.9 17.0 - - + -
92F ILE* 3.9 22.4 - - + -
93F GLN 3.6 9.4 - - - +
94F LEU* 3.5 30.1 - - + -
146F ASN* 5.5 0.4 - - - -
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Residues in contact with SER 28 (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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27F VAL* 1.3 72.9 - - - +
29F VAL* 1.3 61.7 + - - +
30F ARG* 4.0 3.1 + - - +
64F LEU* 3.7 16.6 - - - +
65F GLY 3.7 5.6 - - - -
91F SER 3.8 0.3 - - - +
92F ILE* 3.3 7.4 - - - +
93F GLN* 2.9 53.9 + - - +
146F ASN* 3.2 28.7 + - - -
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Residues in contact with VAL 29 (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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27F VAL* 4.3 0.7 - - + -
28F SER* 1.3 76.2 + - - +
30F ARG* 1.3 60.2 + - - +
31F VAL* 4.1 3.9 + - + +
63F GLY 3.9 0.2 - - - +
64F LEU* 3.5 5.5 - - - +
65F GLY 2.9 36.9 + - - +
66F SER 3.6 28.7 - - - +
67F GLY* 3.7 9.2 - - - +
77F VAL* 4.7 0.7 - - + -
79F THR* 4.4 2.9 - - - +
83F VAL* 4.0 11.1 - - + +
84F ILE* 3.7 29.6 - - + -
90F ILE* 4.0 16.2 - - + -
91F SER 3.6 2.5 - - - -
92F ILE* 4.0 16.8 - - + -
116F LEU* 4.3 5.8 - - + -
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Residues in contact with ARG 30 (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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28F SER* 4.0 4.4 + - - +
29F VAL* 1.3 72.5 - - - +
31F VAL* 1.3 67.3 + - - +
32F GLU* 5.2 8.9 + - + +
62F GLU* 3.1 36.5 + - + +
63F GLY 3.6 7.9 - - - +
64F LEU* 4.4 18.3 - - + +
89F LYS 4.0 0.3 - - - +
90F ILE* 3.5 4.0 - - - +
91F SER* 2.8 56.9 + - - +
93F GLN* 6.5 1.3 - - + -
99F GLU* 6.2 1.8 - - - -
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Residues in contact with VAL 31 (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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29F VAL* 4.2 6.7 - - + +
30F ARG* 1.3 80.3 - - - +
32F GLU* 1.3 65.0 + - - +
61F PHE* 3.7 24.9 - - + -
62F GLU* 3.3 6.2 - - - +
63F GLY* 2.8 39.3 + - - +
83F VAL* 3.6 27.6 - - + +
84F ILE* 3.9 18.6 - - + -
87F ALA* 3.7 31.2 - - + +
89F LYS 3.4 2.2 - - - -
90F ILE* 3.9 6.5 - - + -
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Residues in contact with GLU 32 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30F ARG* 5.2 10.2 + - + +
31F VAL* 1.3 80.3 - - - +
33F GLY* 1.3 52.1 + - - +
61F PHE 3.4 6.3 - - - +
62F GLU* 3.1 34.4 - - + +
87F ALA 3.7 0.2 - - - -
88F GLN* 2.7 30.1 + - + +
89F LYS* 2.9 44.0 + - + +
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Residues in contact with GLY 33 (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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32F GLU* 1.3 75.7 - - - +
34F THR* 1.4 59.4 + - - -
60F PRO* 3.3 23.0 - - - +
61F PHE* 3.2 26.8 + - - -
86F GLN 3.7 10.1 - - - -
88F GLN* 3.7 19.0 - - - +
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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