Contacts of the strand formed by residues 69 - 79 (chain D) in PDB entry 3OF6
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 THR 69 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35D ASP* 5.5 14.8 - - - +
36D VAL 5.0 1.8 - - - -
64D PRO* 3.2 3.6 - - - +
65D ALA* 2.7 34.3 + - - +
67D ASP* 2.7 36.4 + - - +
68D GLY* 1.3 82.3 - - - +
70D TRP* 1.3 76.0 + - - +
71D THR* 5.0 5.2 - - - +
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Residues in contact with TRP 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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35D ASP 4.1 0.9 + - - -
36D VAL* 3.1 47.5 + - + +
37D ALA 3.4 8.5 - - - +
38D PRO* 3.1 47.2 - - + +
39D PRO* 4.8 9.6 - - + -
62D PRO* 3.8 30.3 - - + -
63D SER 3.5 4.3 - - - -
64D PRO* 3.6 40.8 - - + +
68D GLY 5.0 2.5 - - - -
69D THR* 1.3 100.3 + - - +
71D THR* 1.3 68.1 + - - +
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Residues in contact with THR 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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196A ARG* 3.3 29.9 + - - -
32D LEU* 4.3 9.9 - - + -
33D VAL 3.4 12.1 - - - +
34D LEU* 3.6 28.7 - - + -
35D ASP 4.8 1.1 - - - +
36D VAL* 4.7 0.7 - - - -
61D GLY 3.7 2.6 - - - +
62D PRO* 3.3 4.8 - - - +
63D SER* 2.9 32.6 + - - +
65D ALA* 5.3 6.2 - - + +
69D THR* 5.0 7.0 - - - +
70D TRP* 1.3 84.0 - - - +
72D ASN* 1.3 60.3 + - - +
73D LEU* 4.1 0.9 + - - +
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Residues in contact with ASN 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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32D LEU* 4.0 3.3 - - - +
33D VAL* 3.1 45.9 + - + +
36D VAL* 4.7 3.1 - - + +
42D ASP* 4.9 3.4 - - - +
43D SER* 2.8 35.3 + - - +
44D PRO* 4.3 3.4 - - - +
45D ILE* 3.4 16.1 - - - +
59D THR* 4.4 6.6 - - - +
61D GLY* 3.2 23.3 + - - -
62D PRO* 3.9 24.9 - - + +
71D THR* 1.3 72.6 - - - +
73D LEU* 1.3 77.7 + - - +
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Residues in contact with LEU 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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147A VAL* 3.6 32.1 - - + -
149A LEU* 4.0 7.4 - - + -
194A SER* 3.8 25.1 - - - +
195A SER 5.4 0.2 - - - +
196A ARG* 4.9 10.3 - - + +
30D VAL* 3.5 18.2 - - + -
31D CYS 3.3 18.2 - - - +
32D LEU* 3.6 28.7 - - + -
45D ILE* 3.9 2.2 - - - -
59D THR* 3.2 2.6 - - - -
60D TYR* 2.8 37.4 + - + -
61D GLY 4.1 4.2 + - - +
71D THR 5.3 0.9 - - - +
72D ASN* 1.3 85.6 + - - +
74D ALA* 1.3 66.2 + - - +
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Residues in contact with ALA 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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30D VAL* 3.2 3.3 - - - +
31D CYS 3.0 29.6 + - - -
45D ILE* 3.7 25.1 - - + +
47D PHE* 3.4 13.8 - - + -
57D ALA* 5.0 1.1 - - + -
58D PHE 3.2 9.4 - - - +
59D THR* 3.6 23.1 - - + -
60D TYR* 4.6 0.7 - - - -
73D LEU* 1.3 84.2 - - - +
75D HIS* 1.3 60.1 + - - +
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Residues in contact with HIS 75 (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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149A LEU* 4.0 22.2 - - + -
151A THR* 5.0 8.2 - - + +
28D VAL* 4.7 10.5 - - + -
29D VAL 3.3 11.9 - - - +
30D VAL* 4.0 4.7 - - + -
47D PHE* 4.7 0.4 - - - -
57D ALA* 3.1 20.5 - - - +
58D PHE* 2.9 54.1 + + + +
60D TYR* 3.3 30.4 + - + -
74D ALA* 1.3 74.1 - - - +
76D LEU* 1.3 71.6 + - - +
77D SER* 4.5 8.0 - - - -
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Residues in contact with LEU 76 (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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27D MET 3.7 1.0 - - - +
28D VAL* 3.4 4.0 - - - +
29D VAL* 2.7 46.9 + - + +
47D PHE* 4.0 24.9 - - + -
55D LEU* 3.7 42.0 - - + +
56D ASP 3.2 27.6 - - - +
57D ALA* 4.0 10.1 - - + +
75D HIS* 1.3 79.5 - - - +
77D SER* 1.3 73.1 + - - +
78D LEU* 4.3 10.6 - - + +
89D LEU* 4.2 16.2 - - + -
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Residues in contact with SER 77 (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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26D GLN* 2.9 33.4 + - - +
27D MET 3.5 3.8 - - - -
28D VAL* 3.9 10.8 - - - +
75D HIS* 4.5 11.5 - - - -
76D LEU* 1.3 85.4 - - - +
78D LEU* 1.3 64.8 + - - +
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Residues in contact with LEU 78 (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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26D GLN* 3.7 7.0 - - - +
27D MET* 2.8 58.2 + - + +
29D VAL* 6.4 0.4 - - + -
55D LEU* 3.6 32.5 - - + -
76D LEU* 4.3 14.4 - - + +
77D SER* 1.3 77.8 + - - +
79D PRO* 1.3 85.4 - - + +
82D GLU* 5.3 0.7 - - - +
83D LEU* 3.8 11.9 - - + -
86D TRP* 3.9 26.2 - - + +
89D LEU* 5.6 2.7 - - + -
109D LEU* 5.0 5.4 - - + -
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Residues in contact with PRO 79 (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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24D LYS* 5.6 7.9 - - + +
25D GLN 4.0 2.7 - - - +
26D GLN* 3.8 21.3 - - - +
78D LEU* 1.3 103.1 - - + +
80D SER* 1.3 61.7 + - - +
81D GLU* 3.0 32.5 + - + +
82D GLU* 3.4 31.6 + - - +
83D LEU 4.1 1.2 + - - -
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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