Contacts of the strand formed by residues 62 - 68 (chain A) in PDB entry 5WN0
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 62 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A ALA* 3.8 0.8 - - - +
61A THR* 1.3 85.9 + - - +
63A LYS* 1.3 61.5 - - - +
64A ILE* 3.4 32.5 - - + +
90A ASP* 3.6 22.9 - - + +
91A ILE* 4.5 12.8 - - + -
136A ARG* 6.1 1.3 - - - +
165A PHE* 3.9 24.0 - - + -
314A LEU 3.8 0.3 - - - +
315A TYR* 3.5 5.7 - - - +
316A LEU* 2.9 54.4 + - + +
318A LEU* 4.6 10.5 - - + -
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Residues in contact with LYS 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A LEU* 1.3 74.4 - - - +
64A ILE* 1.3 62.0 + - - +
87A GLU* 2.6 61.3 + - - +
88A ALA 4.1 9.2 - - - +
89A PRO* 3.6 6.6 - - + +
90A ASP* 2.8 44.1 + - - +
91A ILE 3.4 4.2 + - - -
301A ARG* 4.2 0.2 - - - +
313A THR* 3.8 12.6 - - + -
314A LEU 3.3 3.8 - - - +
315A TYR* 3.3 44.0 + - + -
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Residues in contact with ILE 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A LEU* 3.4 31.0 - - + -
63A LYS* 1.3 76.7 - - - +
65A CYS* 1.3 67.8 + - - +
91A ILE* 3.5 31.0 - - + +
93A CYS* 4.4 5.4 - - - -
165A PHE* 4.3 9.4 - - + -
167A LEU* 4.0 23.1 - - + -
206A VAL* 4.4 9.6 - - + -
285A PHE* 3.3 20.1 - - + -
313A THR* 3.4 1.9 - - - -
314A LEU* 2.8 56.1 + - + +
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Residues in contact with CYS 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A ILE* 1.3 76.5 - - - +
66A SER* 1.3 63.6 + - - +
67A TRP* 4.9 0.9 - - - -
83A TRP* 3.7 28.0 - - - -
84A VAL* 6.0 0.2 - - - -
87A GLU* 4.7 2.9 - - + -
89A PRO* 3.8 22.2 - - + +
91A ILE 2.8 7.3 + - - +
92A LEU* 3.1 24.9 - - + -
93A CYS* 2.7 32.6 + - - +
311A PRO* 4.1 4.5 - - - -
312A ILE 3.3 12.1 - - - -
313A THR* 3.7 12.8 - - + +
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Residues in contact with SER 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A CYS* 1.3 75.8 - - - +
67A TRP* 1.3 63.4 + - - +
93A CYS* 3.2 5.8 - - - -
95A GLN* 3.1 23.0 + - - -
208A CYS* 4.0 16.7 - - - -
209A GLY* 3.3 17.2 + - - -
283A ASP* 5.6 1.1 + - - +
285A PHE* 4.0 10.5 - - - -
310A CYS 4.7 0.2 - - - +
311A PRO* 3.5 0.9 - - - +
312A ILE* 3.0 48.2 + - - +
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Residues in contact with TRP 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A CYS* 4.9 0.2 - - - -
66A SER* 1.3 79.2 + - - +
68A ASN* 1.3 86.1 + - - +
69A VAL* 3.3 8.7 + - + +
75A TRP* 3.1 46.0 - + - -
80A GLY* 4.1 8.3 - - - -
83A TRP* 3.7 21.8 - + + -
84A VAL* 4.4 3.6 - - + -
92A LEU* 4.9 5.2 - - + -
93A CYS 2.8 11.4 + - - +
94A LEU* 3.2 11.5 - - + -
95A GLN* 2.8 24.2 + - - -
283A ASP* 5.8 0.9 - - - -
304A ALA* 4.1 8.1 - - + -
305A LEU 3.3 31.2 - - - -
306A GLY* 4.6 1.1 - - - -
307A SER* 4.0 3.2 - - - -
309A HIS 3.0 23.7 + - - -
310A CYS 3.7 14.5 - - - -
311A PRO* 3.4 36.6 - - + -
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Residues in contact with ASN 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A TRP* 1.3 81.6 - - - +
69A VAL* 1.3 50.4 + - - +
70A ASP* 2.9 20.3 + - - +
95A GLN* 3.2 25.5 + - + +
96A GLU* 3.0 29.4 + - - +
171A TYR* 3.8 6.3 - - - -
210A ASP* 3.0 25.6 + - - +
283A ASP* 4.2 7.5 + - - +
307A SER* 2.7 24.9 + - - -
309A HIS* 3.4 32.5 + - + +
310A CYS 5.3 0.6 + - - -
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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