Contacts of the strand formed by residues 62 - 68 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B ALA* 3.7 1.0 - - - +
61B THR* 1.3 82.8 - - - +
63B LYS* 1.3 59.9 + - - +
64B ILE* 3.8 22.2 - - + -
90B ASP* 3.7 20.4 - - + -
91B ILE* 4.4 12.6 - - + -
165B PHE* 3.5 37.7 - - + -
314B LEU 3.4 0.9 - - - +
315B TYR* 3.3 9.2 - - - +
316B LEU* 2.9 46.2 + - + +
318B LEU* 3.5 18.8 - - + -
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Residues in contact with LYS 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B LYS* 5.7 1.4 - - - +
62B LEU* 1.3 71.8 - - - +
64B ILE* 1.3 63.4 + - - +
87B GLU* 2.9 60.3 + - - +
88B ALA 4.0 9.2 - - - +
89B PRO* 3.7 7.4 - - + +
90B ASP* 2.8 44.2 + - - +
91B ILE 3.3 5.5 + - - -
301B ARG* 4.7 0.4 - - - +
313B THR* 4.9 3.8 - - + -
314B LEU 3.2 5.8 - - - +
315B TYR* 3.0 43.7 + - + -
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Residues in contact with ILE 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B LEU* 3.8 31.2 - - + -
63B LYS* 1.3 77.3 - - - +
65B CYS* 1.3 70.0 - - - +
91B ILE* 3.5 24.9 - - + +
93B CYS* 4.4 13.2 - - - -
165B PHE* 4.5 4.9 - - + -
167B LEU* 4.2 25.8 - - + -
206B VAL* 4.5 4.3 - - + -
208B CYS* 4.9 0.4 - - - -
285B PHE* 3.3 21.4 - - + -
313B THR* 3.0 5.1 - - - -
314B LEU* 2.6 57.6 + - + +
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Residues in contact with CYS 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B ILE* 1.3 78.7 - - - +
66B SER* 1.3 65.8 + - - +
67B TRP* 5.1 2.2 - - - -
83B TRP* 3.7 25.6 - - - -
87B GLU* 4.7 0.7 - - + -
89B PRO* 3.8 24.2 - - + +
91B ILE 3.0 5.9 + - - +
92B LEU* 3.2 16.0 - - + -
93B CYS 2.9 22.7 + - - -
285B PHE* 4.2 0.7 - - - -
311B PRO* 3.9 11.0 - - - -
312B ILE 3.2 5.8 - - - -
313B THR* 3.5 23.3 - - + -
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Residues in contact with SER 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B CYS* 1.3 74.8 - - - +
67B TRP* 1.3 65.3 + - - +
93B CYS 3.3 6.2 + - - +
95B GLN* 3.2 22.5 + - - -
208B CYS* 3.4 26.9 - - - -
209B GLY* 3.6 6.4 + - - -
283B ASP* 5.7 1.4 + - - +
285B PHE* 3.9 3.6 - - - -
310B CYS 4.5 0.3 - - - +
311B PRO* 3.3 1.2 - - - +
312B ILE* 2.8 54.9 + - - +
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Residues in contact with TRP 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B CYS* 5.1 4.0 - - - -
66B SER* 1.3 77.3 + - - +
68B ASN* 1.3 81.9 + - - +
69B VAL* 3.3 6.3 + - + -
75B TRP* 3.2 47.3 - + - -
80B GLY* 4.2 9.4 - - - -
83B TRP* 3.6 30.3 - + + -
84B VAL* 4.3 5.2 - - + -
92B LEU* 5.5 1.6 - - + -
93B CYS 2.8 10.6 + - - +
94B LEU* 3.1 17.7 - - + +
95B GLN* 3.0 22.6 + - - +
283B ASP* 5.5 1.3 + - - -
304B ALA* 3.9 9.6 - - + -
305B LEU 3.4 27.4 - - - -
306B GLY* 4.7 1.3 - - - -
307B SER* 4.0 3.6 - - - -
309B HIS 3.0 20.6 + - - -
310B CYS 3.7 16.3 - - - -
311B PRO* 3.3 31.6 - - + -
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Residues in contact with ASN 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B TRP* 1.3 75.3 - - - +
69B VAL* 1.3 50.7 + - - +
70B ASP* 3.1 14.9 + - - +
95B GLN* 3.3 19.4 + - + +
96B GLU* 3.0 30.0 + - - +
171B TYR* 3.5 11.5 - - - -
210B ASP* 2.9 27.7 + - - +
283B ASP* 3.9 12.0 + - - +
307B SER* 2.6 28.4 + - - -
309B HIS* 3.5 33.2 + - + +
310B CYS 5.1 0.2 + - - -
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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