Contacts of the strand formed by residues 70 - 78 (chain D) in PDB entry 1PL8
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 70 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41D VAL* 3.3 2.8 - - - -
42D GLY* 2.9 48.7 + - - +
43D ILE 4.5 0.2 - - - -
44D CYS* 3.4 3.0 - - - +
69D HIS* 1.3 82.9 - - + +
71D ALA* 1.3 59.3 + - - +
127D ASN* 4.3 0.2 - - - +
152D ALA* 3.5 21.6 - - - +
155D GLU* 3.2 28.1 - - + +
156D PRO* 3.9 11.6 - - - +
344D LYS* 2.9 34.6 + - - +
346D MET* 5.4 0.7 - - - +
402D ZN 2.2 35.1 - - - -
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Residues in contact with ALA 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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38D MET* 3.3 27.4 - - + -
40D SER 3.2 12.3 - - - +
41D VAL* 3.5 9.4 - - + -
69D HIS 3.7 2.8 + - - -
70D GLU* 1.3 76.5 - - - +
72D SER* 1.3 64.1 + - - +
92D ALA* 3.8 1.9 - - - -
93D ILE* 2.9 34.0 + - + +
127D ASN* 3.7 14.5 + - - +
151D GLY 4.0 4.9 - - - +
152D ALA* 3.9 6.8 + - - +
155D GLU* 5.0 0.8 - - - +
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Residues in contact with SER 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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38D MET* 3.8 6.6 - - - +
39D HIS* 3.1 17.9 + - - -
40D SER* 3.0 15.1 + - - +
71D ALA* 1.3 75.3 - - - +
73D GLY* 1.3 59.8 + - - +
91D VAL 3.1 15.7 - - - -
92D ALA* 4.2 2.2 - - - +
93D ILE* 4.3 7.2 - - - +
142D LEU* 4.4 1.1 - - - -
148D PHE* 2.7 47.0 + - - +
151D GLY* 4.1 6.3 - - - -
152D ALA 3.9 5.8 - - - -
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Residues in contact with GLY 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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36D LEU* 4.9 5.4 - - - -
37D ARG 3.4 13.0 - - - -
38D MET* 4.3 2.7 - - - -
39D HIS* 3.8 9.0 - - - -
72D SER* 1.3 76.8 - - - +
74D THR* 1.3 62.6 + - - -
90D ARG* 3.5 0.2 - - - -
91D VAL* 2.8 37.2 + - - +
93D ILE* 4.5 1.4 - - - +
148D PHE* 3.3 10.9 - - - -
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Residues in contact with THR 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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36D LEU* 3.3 4.3 - - - -
37D ARG* 2.7 76.3 + - - +
39D HIS* 5.1 1.6 - - - +
73D GLY* 1.3 74.9 - - - -
75D VAL* 1.3 70.3 + - - +
88D GLY* 3.7 33.0 - - - +
89D ASP 3.4 4.3 - - - +
90D ARG* 4.9 2.2 - - + +
148D PHE* 3.5 19.8 - - - -
350D ASP* 4.9 2.1 + - - -
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Residues in contact with VAL 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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34D VAL* 4.3 4.9 - - + -
35D LEU 4.2 1.6 - - - +
36D LEU* 3.7 18.8 - - + -
37D ARG* 5.0 0.7 + - - -
74D THR* 1.3 74.0 - - - +
76D GLU* 1.3 60.7 + - - +
77D LYS 3.9 9.0 - - - +
78D VAL* 3.5 32.1 - - + -
85D LEU* 4.5 12.6 - - + -
86D LYS* 3.3 19.1 - - - +
87D PRO* 3.3 3.6 - - + +
88D GLY* 2.7 27.5 + - - -
89D ASP* 2.8 34.2 + - + +
91D VAL* 3.9 12.6 - - + -
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Residues in contact with GLU 76 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35D LEU* 2.7 35.9 + - + +
37D ARG* 2.9 45.0 + - - +
74D THR 3.2 1.0 + - - -
75D VAL* 1.3 73.7 - - - +
77D LYS* 1.3 59.3 + - + +
87D PRO* 3.6 18.5 - - - +
131D PHE* 3.9 21.8 - - + -
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Residues in contact with LYS 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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28D GLU* 2.8 32.8 + - - +
29D PRO* 4.3 16.8 - - + +
34D VAL* 3.3 4.3 - - - +
35D LEU* 2.7 48.8 + - + +
75D VAL* 3.7 0.5 - - - +
76D GLU* 1.3 83.1 - - + +
78D VAL* 1.3 75.6 + - - +
87D PRO* 4.6 5.2 - - - -
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Residues in contact with VAL 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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29D PRO* 4.6 2.7 - - - -
33D GLU 3.7 3.8 - - - -
34D VAL* 3.7 10.1 - - + -
75D VAL* 3.5 27.8 - - + -
77D LYS* 1.3 88.2 - - - +
79D GLY* 1.3 68.9 + - - +
80D SER 3.9 0.3 + - - -
82D VAL* 3.9 17.0 - - + +
85D LEU 3.6 24.0 - - - +
86D LYS* 4.0 7.0 - - - -
87D PRO* 4.3 12.0 - - + +
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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