Contacts of the strand formed by residues 107 - 112 (chain D) in PDB entry 5WYF
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 LYS 107 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16C LYS 4.3 5.7 - - - +
17C TYR* 4.4 4.0 - - - -
98D ALA* 3.5 33.1 + - - +
101D ALA* 3.5 27.2 + - + -
102D PRO* 2.8 25.4 + - - -
103D GLY 3.2 10.9 + - - -
105D SER 3.1 17.8 + - - +
106D PRO* 1.3 75.3 - - - +
108D MET* 1.3 67.8 + - - +
272D GLU* 2.8 31.8 + - - -
273D PRO* 4.7 11.0 - - - -
276D MET* 6.2 1.1 - - - -
292D ILE* 3.8 13.2 - - + -
293D GLY 3.3 18.2 - - - +
294D LYS* 4.2 3.8 - - + +
295D LYS* 3.9 2.5 - - - +
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Residues in contact with MET 108 (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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15C ASN 3.5 19.5 - - - +
16C LYS* 3.6 14.8 - - - +
17C TYR 3.2 9.2 - - - +
18C TYR 3.5 31.9 - - - +
19C ALA* 3.8 8.3 - - - +
20C ARG* 4.5 4.3 - - + +
107D LYS* 1.3 78.1 - - - +
109D VAL* 1.3 69.6 + - - +
292D ILE* 3.6 1.6 - - - +
293D GLY 3.0 30.2 + - - +
295D LYS* 3.9 32.5 - - + +
298D MET* 3.6 22.5 - - + +
299D GLN* 4.1 19.5 - - + +
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Residues in contact with VAL 109 (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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17C TYR 2.7 9.3 + - - +
18C TYR* 3.2 9.2 - - + -
19C ALA* 2.8 27.0 + - - -
94D SER* 3.6 37.7 - - - +
97D LEU* 4.3 3.1 - - + -
98D ALA* 3.6 22.4 - - + +
108D MET* 1.3 82.0 - - - +
110D SER* 1.3 72.8 + - - +
111D PHE* 4.4 8.5 - - + -
290D ALA* 3.9 15.3 - - + -
291D VAL 3.5 8.3 - - - +
292D ILE* 3.9 13.7 - - + -
298D MET* 4.4 1.3 - - - -
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Residues in contact with SER 110 (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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18C TYR* 3.7 4.5 - - - -
19C ALA* 3.8 11.6 - - - +
21C SER* 4.7 0.2 + - - -
22C ALA* 3.5 21.8 + - - +
109D VAL* 1.3 76.1 - - - +
111D PHE* 1.3 61.5 + - - +
125D PHE* 4.3 5.9 - - - -
290D ALA* 3.3 4.3 - - - +
291D VAL* 3.1 47.2 + - - +
298D MET* 4.3 5.6 - - - +
306D HIS* 4.2 19.7 + - - -
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Residues in contact with PHE 111 (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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18C TYR* 3.3 35.2 + + - +
22C ALA* 5.8 0.5 - - - +
82D PRO* 5.5 2.9 - - + -
90D GLY* 3.7 24.5 - - - -
93D LEU* 3.8 26.9 - - + -
94D SER* 3.7 34.1 - - - -
97D LEU* 3.8 18.4 - - + -
109D VAL* 4.4 4.3 - - + -
110D SER* 1.3 75.2 - - - +
112D GLY* 1.3 58.9 - - - +
288D LEU* 4.0 9.2 - - + -
289D SER 3.4 13.9 - - - +
290D ALA* 4.3 3.6 - - + -
291D VAL* 6.1 0.2 - - - -
306D HIS* 4.3 10.9 + - - +
307D LEU* 5.2 2.3 - - - -
308D PHE* 4.1 8.8 + - - -
311D ALA* 3.6 8.6 - - + +
312D GLY* 3.7 33.2 - - - +
317D SER* 5.0 0.2 - - - -
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Residues in contact with GLY 112 (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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110D SER 4.0 0.2 + - - -
111D PHE* 1.3 73.7 - - - +
113D ASN* 1.3 58.8 + - - -
117D ASP* 3.1 15.3 - - - -
118D ALA* 6.1 0.2 - - - +
288D LEU* 3.7 10.0 - - - +
289D SER* 2.9 38.9 + - - +
290D ALA* 4.5 0.4 - - - +
306D HIS* 5.1 1.1 + - - -
308D PHE* 4.1 4.3 - - - -
311D ALA* 3.5 18.0 - - - +
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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