Contacts of the strand formed by residues 69 - 74 (chain D) in PDB entry 4WFH
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 SER 69 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D THR* 6.0 1.7 - - - +
23D CYS 3.8 3.1 - - - -
24D SER* 4.6 4.3 - - - +
65D GLY* 3.2 5.0 - - - -
66D SER 3.0 25.2 + - - +
67D GLY 3.6 0.6 - - - -
68D THR* 1.3 87.0 - - - +
70D TYR* 1.3 65.4 + - - +
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Residues in contact with TYR 70 (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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22D THR* 3.3 5.9 - - - +
23D CYS 2.7 34.8 + - - +
25D ALA* 5.7 0.2 - - + -
29D VAL* 2.7 36.2 + - + -
30D SER* 3.6 11.7 + - - -
31D TYR 4.5 2.0 - - - -
32D MET* 3.6 42.6 - - + -
34D TRP* 4.2 5.2 - - + +
50D THR* 3.6 23.6 - - + -
64D SER 3.4 6.3 - - - +
65D GLY* 3.4 16.8 - - - -
66D SER* 3.3 22.3 - - - -
67D GLY 3.2 29.1 + - - -
68D THR 4.3 1.3 - - - -
69D SER* 1.3 81.5 + - - +
71D SER* 1.3 62.7 + - - +
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Residues in contact with SER 71 (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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20D THR* 4.4 13.4 - - - +
21D MET 3.2 10.5 - - - -
22D THR* 4.5 7.4 - - - -
34D TRP* 3.6 10.1 + - - -
63D GLY* 3.4 4.2 - - - -
64D SER* 2.8 45.8 + - - +
70D TYR* 1.3 76.2 - - - +
72D LEU* 1.3 60.0 + - - +
73D THR* 4.0 10.7 + - - -
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Residues in contact with LEU 72 (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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19D VAL 4.0 0.2 - - - +
20D THR* 3.4 2.6 - - - +
21D MET* 2.7 50.8 + - + +
34D TRP* 3.6 47.1 - - + -
46D TRP* 4.9 3.8 - - + -
47D ILE* 4.1 13.2 - - + -
61D PHE* 3.8 20.4 - - + -
62D SER 3.6 9.4 - - - +
63D GLY* 4.6 0.4 - - - -
71D SER* 1.3 73.9 - - - +
73D THR* 1.3 95.3 + - - +
74D ILE* 4.5 0.2 - - + -
85D TYR* 3.7 30.7 - - + -
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Residues in contact with THR 73 (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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18D LYS* 4.6 14.8 - - + +
19D VAL 3.2 10.5 - - - +
20D THR* 3.8 17.2 + - - +
60D ARG 3.5 0.9 - - - +
61D PHE* 3.3 4.5 - - - -
62D SER* 2.9 47.8 + - - +
71D SER* 4.0 11.8 + - - -
72D LEU* 1.3 79.2 + - - +
74D ILE* 1.3 76.9 + - - +
75D SER* 4.3 3.8 - - - +
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Residues in contact with ILE 74 (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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17D GLU 4.3 0.2 - - - +
18D LYS* 3.3 3.8 - - - +
19D VAL* 2.7 49.8 + - + +
21D MET* 4.4 4.5 - - + -
60D ARG* 3.4 15.7 - - + -
61D PHE* 3.4 34.8 - - + -
72D LEU* 4.5 4.0 - - + -
73D THR* 1.3 78.2 - - - +
75D SER* 1.3 67.0 + - - +
76D SER 3.8 20.4 - - - +
77D MET* 3.9 5.6 - - - +
81D ASP* 3.7 23.3 - - + +
85D TYR* 4.3 1.6 - - - +
103D LEU* 4.0 27.6 - - + -
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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