Contacts of the strand formed by residues 62 - 69 (chain D) in PDB entry 3FUB
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 GLU 62 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155C LEU* 6.1 0.2 - - + -
159C LYS* 3.4 44.5 + - + +
162C ASN* 3.4 26.4 + - - +
163C LEU* 4.5 7.6 - - + -
47D HIS* 2.6 40.1 + - - +
48D LEU 3.3 12.8 - - - +
49D ASN* 3.7 21.3 - - - +
50D VAL* 4.2 4.6 - - - +
60D LYS 3.9 7.1 - - - +
61D GLU* 1.3 79.7 - - - +
63D LEU* 1.3 65.6 + - - +
1E NAG 4.5 10.4 + - - +
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Residues in contact with LEU 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162C ASN* 5.0 1.1 - - - -
163C LEU* 4.1 8.5 - - - +
47D HIS* 3.5 4.5 - - - -
48D LEU* 2.7 56.1 + - + +
49D ASN 3.6 20.2 - - - +
50D VAL* 3.9 13.2 - - + -
53D LEU* 3.7 33.2 - - + -
62D GLU* 1.3 76.7 - - - +
64D ILE* 1.3 64.3 + - - +
65D PHE* 4.2 14.4 - - + +
111D LEU* 3.4 22.9 - - + -
123D LEU* 4.5 3.1 - - + -
126D HIS* 4.0 25.4 - - + +
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Residues in contact with ILE 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162C ASN 5.1 4.2 + - - +
163C LEU* 3.8 39.7 - - + +
168C LYS* 6.0 0.3 + - - +
45D ALA* 4.3 21.1 - - + -
46D ILE 3.8 8.1 - - - +
47D HIS* 3.8 26.2 - - + -
63D LEU* 1.3 80.2 - - - +
65D PHE* 1.3 62.4 + - - +
66D ARG* 4.6 9.1 + - + +
111D LEU* 4.9 3.9 - - - +
126D HIS* 4.8 2.9 + - - -
127D SER* 4.3 9.7 + - - -
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Residues in contact with PHE 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D THR 3.9 0.3 - - - +
45D ALA* 3.5 0.9 - - - -
46D ILE* 2.9 50.2 + - + +
48D LEU* 4.1 20.0 - - + -
53D LEU* 4.7 12.3 - - + -
63D LEU* 4.0 11.6 - - + -
64D ILE* 1.3 74.5 - - - +
66D ARG* 1.3 68.6 + - - +
67D TYR* 3.9 32.5 - + + -
126D HIS* 3.0 32.8 - + - -
127D SER* 4.1 6.1 - - - -
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Residues in contact with ARG 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D LEU* 3.5 35.0 - - + +
44D THR* 3.0 5.2 - - - +
45D ALA* 3.4 31.6 - - + -
64D ILE* 4.6 8.7 + - + +
65D PHE* 1.3 81.5 - - - +
67D TYR* 1.3 60.2 - - - +
108D ASP* 2.5 42.2 + - - -
127D SER* 2.9 13.0 + - - +
128D ALA* 2.8 43.8 + - - +
129D LYS* 4.2 9.3 + - - +
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Residues in contact with TYR 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D VAL 3.8 0.5 - - - +
43D LEU* 3.8 1.1 - - - -
44D THR* 2.8 66.7 + - + +
46D ILE* 4.1 22.4 - - + +
65D PHE* 3.9 31.0 - + + -
66D ARG* 1.3 74.1 - - - +
68D CYS* 1.3 65.8 + - - +
69D SER* 3.6 28.3 - - - -
104D PRO* 6.2 0.2 - - - -
128D ALA* 4.4 3.6 - - - -
131D CYS* 4.6 0.7 - - - -
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Residues in contact with CYS 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D VAL 3.4 4.9 - - - -
67D TYR* 1.3 74.4 - - - +
69D SER* 1.3 64.0 + - - +
102D CYS* 3.7 28.0 - - - +
103D ARG* 4.1 3.6 - - - -
104D PRO* 3.7 26.5 - - + +
128D ALA* 3.8 12.1 - - - +
131D CYS* 2.0 52.7 - - + -
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Residues in contact with SER 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D VAL* 3.2 34.9 + - - +
44D THR* 3.8 10.9 + - - -
67D TYR* 3.6 26.3 + - - -
68D CYS* 1.3 75.6 - - - +
70D GLY* 1.3 58.8 + - - +
102D CYS* 3.9 8.6 - - - -
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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