Contacts of the strand formed by residues 116 - 120 (chain b) in PDB entry 5W97
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 116 (chain b).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109b GLU* 3.6 0.5 - - - +
110b TYR* 2.9 48.2 + - + +
111b THR* 4.5 0.7 - - - +
114b GLU* 2.9 11.6 + - + +
115b ASP* 1.3 68.8 - - - +
117b SER* 1.3 70.2 + - - +
118b PHE* 3.8 30.5 - - + -
222b TRP* 4.2 9.4 - - + -
223b SER* 3.4 45.5 - - - +
226b MET* 3.9 24.9 - - + +
227b LEU* 4.9 14.4 - - + -
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Residues in contact with SER 117 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108b TYR 3.2 16.7 + - - -
109b GLU* 4.1 13.1 - - - +
115b ASP 3.9 4.4 + - - -
116b LEU* 1.3 83.0 - - - +
118b PHE* 1.3 65.2 + - - +
66h ILE* 4.3 14.1 - - - +
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Residues in contact with PHE 118 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107b SER* 3.4 2.6 - - - -
108b TYR* 2.9 52.3 + + + +
110b TYR* 3.8 26.2 - + - -
116b LEU* 3.8 12.8 - - + -
117b SER* 1.3 78.4 + - - +
119b ASP* 1.3 86.1 + - - +
140b ASN* 3.8 16.2 - - + +
141b ARG 3.6 26.9 - - - -
142b VAL* 4.8 0.2 - - - -
222b TRP* 3.6 29.2 - + - -
226b MET* 4.1 22.2 - - + -
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Residues in contact with ASP 119 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105b TYR* 3.4 30.3 + - + -
106b TRP 3.6 5.6 - - - -
107b SER* 4.0 7.6 - - - +
118b PHE* 1.3 94.5 - - - +
120b SER* 1.3 64.4 + - - +
121b TYR* 3.6 26.1 + - + -
139b ASP* 4.7 1.3 - - - -
140b ASN* 3.5 12.5 + - - +
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Residues in contact with SER 120 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105b TYR* 3.6 4.9 - - - +
106b TRP* 3.0 32.8 + - - +
108b TYR* 3.8 22.6 + - - -
118b PHE* 4.8 0.2 - - - -
119b ASP* 1.3 80.0 - - - +
121b TYR* 1.3 62.0 + - - +
138b VAL* 3.7 16.3 - - - +
139b ASP* 3.4 7.6 - - - -
140b ASN* 3.1 23.7 + - - -
142b VAL* 5.6 0.5 - - - +
208b PRO 4.8 5.0 + - - +
209b ILE* 5.7 1.2 - - - -
210b VAL 5.8 0.3 + - - -
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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