Contacts of the strand formed by residues 54 - 61 (chain X) in PDB entry 2AW2
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 PHE 54 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A GLN* 5.2 9.6 - - - -
46X HIS* 3.7 30.3 - + + -
48X ILE* 3.5 33.9 - - + -
53X PRO* 1.3 78.4 - - - +
55X GLU* 1.3 89.6 + - - +
56X LEU* 3.8 8.3 - - + -
101X HIS* 3.9 1.0 + - - -
102X PHE* 2.7 49.2 + + + +
103X GLU* 5.4 0.5 - - - +
105X VAL* 3.4 20.6 - - + -
131X LEU* 3.6 24.7 - - + -
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Residues in contact with GLU 55 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A LYS* 5.5 1.2 + - - -
46X HIS* 6.0 0.3 - - - -
54X PHE* 1.3 100.0 - - - +
56X LEU* 1.3 60.6 + - - +
57X GLU* 4.2 19.7 + - - +
99X ILE* 3.5 35.3 - - + +
100X LEU 3.2 7.2 - - - +
101X HIS* 3.7 19.8 + - - +
102X PHE* 4.7 0.2 - - - -
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Residues in contact with LEU 56 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A LYS* 5.0 2.2 - - - +
46X HIS* 3.5 35.2 - - + +
54X PHE* 3.8 5.8 - - + -
55X GLU* 1.3 73.4 - - - +
57X GLU* 1.3 60.8 + - - +
58X CYS 4.0 0.4 - - - -
71X TRP* 3.8 16.5 - - + -
98X PHE 3.7 1.7 - - - +
99X ILE* 3.2 4.5 - - - -
100X LEU* 2.8 37.8 + - + -
102X PHE* 4.3 12.5 - - + -
113X TYR* 4.0 29.6 - - + -
129X THR* 3.6 27.6 - - + -
131X LEU* 3.8 21.1 - - + -
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Residues in contact with GLU 57 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A LYS* 3.3 28.3 + - - +
14B GLU* 4.6 5.7 - - - +
31B GLU* 3.2 29.0 - - - +
40X ILE* 4.8 3.5 - - - +
55X GLU* 4.2 21.9 - - - +
56X LEU* 1.3 77.2 - - - +
58X CYS* 1.3 59.5 + - - +
59X PRO* 3.2 14.6 - - - +
71X TRP* 4.2 2.7 - - - -
90X LYS* 3.1 27.4 + - - -
97X PHE* 3.9 16.3 - - + +
98X PHE 3.8 3.8 - - - -
99X ILE* 4.1 20.8 - - + +
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Residues in contact with CYS 58 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38X LEU* 3.9 21.1 - - - -
40X ILE* 4.5 1.8 - - - -
57X GLU* 1.3 69.9 - - - +
59X PRO* 1.4 66.9 - - - +
60X VAL* 3.4 8.0 + - - +
69X VAL* 4.5 4.3 - - - -
71X TRP* 3.4 19.8 - - + +
97X PHE* 3.5 1.4 - - - -
98X PHE* 2.9 39.2 + - + +
115X CYS* 2.0 49.8 - - + -
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Residues in contact with PRO 59 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A LYS* 5.3 7.4 - - + -
32B LEU* 3.7 17.9 - - + -
38X LEU* 3.5 7.1 - - - +
39X TYR* 3.0 53.0 + - + +
40X ILE* 3.8 13.9 - - + -
57X GLU 3.2 11.2 - - - +
58X CYS* 1.4 81.4 - - - +
60X VAL* 1.3 59.2 + - - +
61X LYS 4.2 0.2 - - - -
95X ILE* 3.7 22.9 - - + -
96X SER 3.5 6.5 - - - +
97X PHE* 3.8 13.7 - - + -
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Residues in contact with VAL 60 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36X VAL* 5.1 1.8 - - + -
38X LEU* 3.6 26.7 - - + -
58X CYS* 3.5 20.0 - - - +
59X PRO* 1.3 70.8 - - - +
61X LYS* 1.3 65.8 + - - +
62X TYR* 4.0 20.0 + - + -
67X PRO* 4.2 21.1 - - + -
69X VAL* 4.5 7.2 - - + -
89X TRP* 4.0 27.1 - - + -
95X ILE* 3.6 5.7 - - - +
96X SER* 2.7 38.2 + - - +
98X PHE 4.5 1.1 - - - +
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Residues in contact with LYS 61 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A LYS* 5.9 7.6 - - - +
34X CYS* 3.4 30.7 - - - +
35X ASP 4.2 14.0 + - - +
36X VAL* 3.4 6.9 - - - +
37X GLN 3.1 28.4 + - - +
39X TYR* 3.4 42.2 - - + +
59X PRO 4.2 0.4 - - - -
60X VAL* 1.3 73.3 - - - +
62X TYR* 1.3 70.5 + - - +
94X ASN 4.6 15.5 + - - +
95X ILE* 5.1 5.8 - - + -
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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