Contacts of the strand formed by residues 62 - 71 (chain U) in PDB entry 2FD6
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 62 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A TRP* 5.7 2.6 - - - +
31A CYS 4.8 3.8 + - - -
32A ASN* 3.2 33.3 + - - +
33A CYS 5.5 0.4 - - - +
31U LEU* 4.5 20.3 - - + +
32U TRP 3.2 21.5 - - - +
33U GLU* 3.7 24.9 + - + -
58U ARG* 3.3 7.4 - - - +
59U THR* 3.1 43.7 + - + +
60U GLY 3.5 0.6 - - - -
61U LEU* 1.3 84.0 - - - +
63U ILE* 1.3 77.1 + - - +
64U THR* 3.8 19.7 + - - +
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Residues in contact with ILE 63 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30U ARG 3.3 5.0 - - - +
31U LEU* 3.6 1.0 - - - -
32U TRP* 3.1 60.7 + - + +
56U SER* 4.0 18.6 - - - +
57U TYR 3.6 10.5 - - - +
58U ARG* 3.9 31.4 - - + +
61U LEU 4.3 0.9 - - - +
62U LYS* 1.3 85.0 - - - +
64U THR* 1.3 61.5 + - - +
65U SER* 4.1 7.5 + - - +
113U LEU* 5.3 5.8 - - + -
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Residues in contact with THR 64 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A TRP* 4.1 15.6 + - + +
29U VAL* 4.3 5.8 - - + -
30U ARG 3.4 6.3 - - - +
31U LEU* 4.6 5.2 - - + +
55U LEU 3.9 0.7 - - - +
56U SER* 3.2 4.5 + - - -
57U TYR* 2.9 70.9 + - + +
59U THR* 4.9 2.4 - - - +
62U LYS* 3.8 19.4 + - - +
63U ILE* 1.3 74.4 - - - +
65U SER* 1.3 62.9 + - - +
66U LEU* 4.0 22.7 - - + -
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Residues in contact with SER 65 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28U ILE 3.4 6.4 - - - +
30U ARG* 2.9 51.3 + - - +
54U THR* 6.2 1.8 - - - -
55U LEU 3.6 3.6 - - - -
56U SER* 3.2 18.7 + - - -
63U ILE* 4.1 9.7 + - - +
64U THR* 1.3 72.6 - - - +
66U LEU* 1.3 63.8 + - - +
67U THR* 4.0 7.6 - - - +
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Residues in contact with LEU 66 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A ASN* 3.3 42.0 - - + +
25A PHE* 3.5 24.5 - - + -
28A ILE* 5.1 1.3 - - + -
30A TRP* 3.6 17.5 - - + -
28U ILE 3.4 2.2 - - - -
29U VAL* 3.4 42.4 - - + -
54U THR* 3.4 4.0 - - - +
55U LEU* 2.8 43.7 + - + +
57U TYR* 4.6 8.5 - - + +
64U THR* 4.0 10.1 - - + -
65U SER* 1.3 70.7 - - - +
67U THR* 1.3 66.7 + - - +
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Residues in contact with THR 67 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A PHE* 3.3 5.0 - - - -
26U THR 3.6 1.7 - - - +
27U THR* 3.6 1.2 - - - -
28U ILE* 2.8 55.3 + - + +
30U ARG* 3.7 25.6 - - - +
53U ARG 3.4 7.4 + - - -
54U THR* 4.0 16.2 + - + -
65U SER* 4.0 7.4 - - - +
66U LEU* 1.3 80.3 - - - +
68U GLU* 1.3 62.1 + - - +
69U VAL* 4.6 9.7 - - - +
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Residues in contact with GLU 68 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A TYR 4.3 4.1 - - - +
25A PHE* 3.5 29.1 - - + -
26A SER* 2.8 27.2 + - - -
25U ARG* 4.5 13.2 - - + +
26U THR 3.5 5.6 - - - +
27U THR* 2.9 18.0 + - - +
50U LYS* 3.9 25.8 + - - +
51U THR 4.5 4.3 - - - +
52U ASN* 3.2 6.5 - - - +
53U ARG* 2.9 41.7 + - + +
67U THR* 1.3 75.5 + - - +
69U VAL* 1.3 70.9 + - - +
70U VAL* 4.5 8.1 - - + +
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Residues in contact with VAL 69 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B NAG 4.2 9.9 - - - +
2B FUC 4.7 22.2 - - + +
24U CYS 3.8 0.2 - - - +
25U ARG* 3.4 5.0 - - - +
26U THR* 3.1 52.7 + - + +
28U ILE* 5.9 4.3 - - + -
52U ASN* 3.2 13.7 - - + +
67U THR* 4.6 10.8 - - - +
68U GLU* 1.3 76.2 - - - +
70U VAL* 1.3 65.6 + - - +
71U CYS* 5.7 1.2 - - - -
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Residues in contact with VAL 70 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B NAG 3.0 24.8 + - - +
23U LEU* 3.2 41.7 - - + -
24U CYS 3.2 14.4 - - - +
25U ARG* 4.1 10.8 - - + -
46U THR* 4.4 0.2 - - + -
50U LYS* 4.1 22.9 - - + +
51U THR* 4.3 17.3 - - - +
52U ASN* 2.8 11.2 + - - +
68U GLU* 4.5 5.4 - - + -
69U VAL* 1.3 80.5 - - - +
71U CYS* 1.3 79.7 + - - +
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Residues in contact with CYS 71 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B NAG 6.0 4.3 - - - +
23U LEU* 3.4 7.3 - - - -
24U CYS* 2.7 37.5 + - - +
25U ARG* 6.0 0.2 - - - -
69U VAL* 5.7 1.6 - - - -
70U VAL* 1.3 82.7 - - - +
72U GLY* 1.3 59.0 + - - +
73U LEU* 4.6 1.3 - - + +
76U CYS* 2.0 59.4 - - + -
77U ASN* 4.6 1.8 - - - -
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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