Contacts of the strand formed by residues 61 - 71 (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 PHE 61 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31F VAL* 3.7 25.1 - - + -
32F GLU* 3.4 7.3 - - - +
33F GLY* 3.2 33.3 + - - +
34F THR 3.3 44.0 - - - -
59F GLN* 4.6 2.0 - - - +
60F PRO* 1.3 75.1 - - - +
62F GLU* 1.3 65.6 + - - +
63F GLY* 3.9 11.7 - - - -
86F GLN* 3.7 45.1 - - + -
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Residues in contact with GLU 62 (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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30F ARG* 3.1 34.0 + - + +
31F VAL 3.3 3.8 - - - +
32F GLU* 3.1 37.2 - - + +
61F PHE* 1.3 77.6 - - - +
63F GLY* 1.3 59.0 - - - +
64F LEU 4.5 0.2 + - - -
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Residues in contact with GLY 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29F VAL 4.5 0.2 - - - -
30F ARG* 3.6 6.4 - - - +
31F VAL* 2.8 40.2 + - - +
61F PHE* 3.9 14.0 - - - -
62F GLU* 1.3 74.7 - - - +
64F LEU* 1.3 63.6 + - - +
83F VAL* 5.9 2.2 - - - -
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Residues in contact with LEU 64 (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* 3.7 17.5 - - - +
29F VAL 3.5 6.3 - - - +
30F ARG* 4.4 21.1 - - + +
62F GLU 4.5 0.2 + - - -
63F GLY* 1.3 71.7 - - - +
65F GLY* 1.3 71.7 + - - +
83F VAL* 5.1 2.5 - - - -
146F ASN* 3.8 25.6 - - + +
149F GLY* 4.2 18.8 - - - +
185F GLY* 3.8 16.0 + - - -
187F SER* 5.6 0.2 + - - -
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Residues in contact with GLY 65 (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* 3.7 5.5 - - - -
29F VAL* 2.9 27.3 + - - +
64F LEU* 1.3 82.7 - - - +
66F SER* 1.3 65.3 + - - -
83F VAL* 4.2 15.0 - - - +
146F ASN* 3.7 2.1 - - - +
185F GLY* 3.3 13.5 - - - -
187F SER* 3.9 7.2 - - - -
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Residues in contact with SER 66 (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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26F VAL* 5.0 0.9 - - - -
27F VAL 3.3 12.6 - - - -
29F VAL* 3.6 9.7 - - - +
65F GLY* 1.3 71.6 + - - -
67F GLY* 1.3 55.2 + - - +
79F THR* 2.6 28.1 + - - -
144F VAL 4.9 0.2 - - - -
145F GLY* 3.2 8.5 - - - -
146F ASN* 2.7 30.8 + - - -
185F GLY 2.9 8.0 + - - -
186F ASN 3.9 0.8 + - - -
187F SER 2.9 12.6 + - - +
188F GLY* 3.4 5.0 - - - -
189F GLY* 3.6 22.9 - - - -
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Residues in contact with GLY 67 (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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26F VAL* 3.5 11.3 - - - +
27F VAL* 2.8 42.3 + - - +
29F VAL* 3.7 3.9 - - - +
66F SER* 1.3 75.2 - - - +
68F VAL* 1.4 63.8 + - - -
77F VAL* 3.9 5.6 - - - -
78F LEU 3.2 11.9 - - - -
79F THR* 4.3 0.4 - - - -
188F GLY 3.5 2.9 - - - -
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Residues in contact with VAL 68 (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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25F ALA 3.6 5.8 - - - +
26F VAL* 4.8 1.6 - - + -
67F GLY* 1.4 78.4 - - - +
69F ILE* 1.4 65.8 + - - +
70F ILE* 3.2 4.0 + - + +
77F VAL* 3.3 5.3 - - - +
78F LEU* 2.8 37.8 + - + +
127F ILE* 3.7 42.0 - - + -
189F GLY 3.7 1.1 - - - -
190F ALA* 3.6 30.7 - - + +
198F LEU* 4.1 9.4 - - + -
201F ILE* 3.5 30.3 - - + -
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Residues in contact with ILE 69 (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 3.8 10.5 - - - +
25F ALA 2.6 17.9 + - - +
27F VAL* 3.6 28.5 - - + -
68F VAL* 1.4 68.3 - - - +
70F ILE* 1.3 61.7 + - - +
71F ASN 3.9 5.6 - - - +
72F ALA* 3.9 27.4 - - - +
76F TYR 3.5 7.6 - - - +
77F VAL* 4.0 12.6 - - + -
94F LEU* 4.2 7.4 - - + -
118F ILE* 4.7 2.9 - - + -
124F LEU* 4.0 25.4 - - + -
125F THR 3.3 28.3 - - - +
126F GLN* 3.5 0.8 - - - -
127F ILE* 2.9 33.3 + - - +
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Residues in contact with ILE 70 (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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68F VAL* 3.2 7.1 + - + +
69F ILE* 1.3 75.3 - - - +
71F ASN* 1.4 62.3 + - + +
76F TYR* 2.8 31.0 + - + +
78F LEU* 3.6 32.5 - - + +
115F LEU* 4.3 11.7 - - + -
126F GLN* 3.9 16.7 + - - +
127F ILE* 4.3 12.1 - - + +
129F ILE* 3.7 35.0 - - + +
198F LEU* 5.3 1.8 - - + -
225F ARG* 4.8 6.1 - - + -
228F ALA* 4.1 14.6 - - + -
232F ILE* 6.0 1.6 - - + -
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Residues in contact with ASN 71 (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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69F ILE* 3.9 3.4 - - - +
70F ILE* 1.4 78.6 - - + +
72F ALA* 1.3 52.5 + - - +
73F SER* 3.1 14.6 + - - -
74F LYS* 3.0 40.1 + - - +
75F GLY* 2.8 31.0 + - - -
76F TYR* 3.0 37.2 + - + -
126F GLN* 3.4 8.0 + - - +
232F ILE* 6.0 1.8 - - - +
229J GLN* 4.9 8.1 + - - +
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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