Contacts of the strand formed by residues 50 - 59 (chain D) in PDB entry 5AEW
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 LEU 50 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46D TRP* 3.9 35.7 - - + +
47D PHE* 3.0 41.0 + - + +
48D ALA* 4.1 5.4 - - - +
49D LEU* 1.3 76.5 - - - +
51D ASP* 1.3 70.7 + - - +
52D LYS* 3.7 0.9 + - - +
54D ILE* 4.2 21.3 - - + -
56D TYR* 5.2 5.4 - - + -
86D HIS* 3.9 13.8 + - + -
89D MET* 4.1 20.9 - - + -
166D SER* 4.9 1.1 - - - -
167D ILE* 3.8 31.6 - - + -
170D ARG* 5.8 0.2 - - - +
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Residues in contact with ASP 51 (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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162B ASN* 2.6 18.0 + - - +
49D LEU 3.5 3.4 + - - -
50D LEU* 1.3 76.2 - - - +
52D LYS* 1.3 66.2 + - - +
53D ASP* 2.3 32.1 + - - +
54D ILE* 3.0 21.7 + - - +
86D HIS* 3.6 1.6 - - - -
157D ARG* 2.6 24.6 + - - -
166D SER* 3.3 20.9 + - - +
167D ILE 2.9 21.5 + - - +
168D ALA* 3.8 7.4 - - - -
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Residues in contact with LYS 52 (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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160B ASP* 3.2 43.3 + - - +
161B ASN* 3.4 27.1 - - - +
162B ASN* 3.4 23.0 - - - +
50D LEU 3.7 1.2 + - - +
51D ASP* 1.3 75.4 - - - +
53D ASP* 1.3 56.7 + - - +
54D ILE 3.3 1.5 + - - -
86D HIS* 3.4 34.5 + - + +
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Residues in contact with ASP 53 (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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45B ALA* 4.4 8.1 - - - +
48B ALA* 4.1 25.5 - - + +
49B LEU* 6.3 2.5 - - + -
161B ASN* 4.4 9.9 - - + -
162B ASN* 3.4 19.8 - - + +
51D ASP* 2.3 32.1 + - - +
52D LYS* 1.3 77.0 - - - +
54D ILE* 1.3 65.6 + - - +
55D HIS* 3.2 16.4 + - - -
157D ARG* 3.0 26.6 + - - -
168D ALA 3.5 8.4 - - - +
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Residues in contact with ILE 54 (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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50D LEU* 4.2 27.1 - - + -
51D ASP 3.0 20.4 + - - +
52D LYS 3.3 0.4 - - - +
53D ASP* 1.3 77.6 + - - +
55D HIS* 1.3 78.7 + - - +
56D TYR* 4.2 12.1 - - + -
85D THR* 3.6 18.6 - - - +
86D HIS* 3.5 29.2 + - + +
89D MET* 4.9 1.6 - - + -
167D ILE* 3.2 38.1 - - + +
168D ALA 3.2 20.2 + - - +
169D LYS* 3.7 6.3 - - - +
170D ARG* 4.2 4.9 - - + +
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Residues in contact with HIS 55 (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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47B PHE* 6.6 0.4 - + - -
48B ALA* 3.6 34.4 + - + +
50B LEU 5.1 7.6 - - - -
52B LYS* 5.7 9.1 - - + -
86B HIS* 5.4 9.0 - + - -
53D ASP* 3.2 27.6 + - - -
54D ILE* 1.3 78.1 + - - +
56D TYR* 1.3 61.0 - - - +
57D PHE* 4.0 4.0 - - + +
83D ASP* 5.3 7.2 + - - +
84D GLU 3.5 7.7 + - - +
85D THR* 4.8 15.0 - - + +
168D ALA 3.5 5.6 + - - +
169D LYS* 3.6 20.4 - - + +
170D ARG 3.0 26.9 + - - +
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Residues in contact with TYR 56 (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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46D TRP* 4.2 24.7 - + - -
50D LEU* 5.2 3.8 - - + -
54D ILE* 4.2 16.4 - - + -
55D HIS* 1.3 72.4 - - - +
57D PHE* 1.3 60.4 + - - +
82D PHE* 4.1 30.7 - + + -
83D ASP* 3.3 5.3 + - - -
84D GLU* 2.8 45.4 + - + +
89D MET* 4.0 23.8 - - + -
170D ARG* 3.4 33.0 - - + -
172D ILE* 3.8 15.9 - - + -
187D PHE* 3.8 7.5 - + - +
188D PHE* 2.8 38.5 + - - +
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Residues in contact with PHE 57 (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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249A PRO* 6.5 0.4 - - + -
250A GLU* 4.0 13.7 - - - -
52B LYS* 5.1 5.4 - - - -
371C ARG* 5.6 0.9 - - - -
55D HIS* 5.0 3.4 - - + +
56D TYR* 1.3 77.3 - - - +
58D MET* 1.3 56.0 + - - +
59D PRO* 3.7 33.9 - - + -
74D SER* 4.3 10.3 - - - -
75D GLY 4.5 14.6 - - - -
76D ASP* 5.7 0.9 - - - -
80D ALA* 3.7 23.1 - - + -
82D PHE* 3.4 12.6 - - - -
83D ASP* 3.7 24.2 - - - +
169D LYS* 6.3 0.7 - - - +
170D ARG 2.8 13.8 + - - +
171D THR* 3.1 24.5 - - + +
172D ILE* 2.8 34.2 + - - +
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Residues in contact with MET 58 (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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57D PHE* 1.3 73.3 - - - +
59D PRO* 1.3 65.4 - - - +
80D ALA* 3.6 1.0 - - - +
81D HIS* 3.0 51.5 + - + +
82D PHE* 3.0 34.8 + - + +
172D ILE* 3.5 39.9 - - + +
174D LEU* 4.0 25.8 - - + -
184D LEU* 4.1 5.8 - - - -
188D PHE* 3.4 40.4 - - + -
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Residues in contact with PRO 59 (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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250A GLU* 4.3 4.7 - - - +
57D PHE* 3.7 36.3 - - + +
58D MET* 1.3 93.9 - - - +
60D LEU* 1.3 68.3 + - - +
61D ARG* 3.8 3.3 + - - +
73D TYR* 3.7 22.9 - - + -
74D SER* 3.3 20.9 - - - +
80D ALA* 4.3 1.3 - - + -
81D HIS* 3.5 10.4 - - - -
171D THR* 4.1 4.0 - - + -
172D ILE 3.4 12.0 - - - +
173D LEU* 3.7 12.5 - - + -
174D LEU* 5.7 2.6 + - - +
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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