Contacts of the strand formed by residues 118 - 122 (chain F) in PDB entry 5DK3
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 SER 118 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116F ALA 3.7 3.0 + - - -
117F PRO* 1.3 69.8 - - - +
119F VAL* 1.4 58.7 + - - +
120F PHE* 3.3 31.7 - - - -
139F LEU 3.6 0.2 - - - +
141F ASN* 2.9 36.1 + - - -
142F ASN* 5.2 3.6 + - - +
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Residues in contact with VAL 119 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117F PRO* 3.3 20.0 + - + +
118F SER* 1.4 72.9 - - - +
120F PHE* 1.3 73.8 + - - +
138F CYS* 3.8 22.9 - - - -
139F LEU 3.3 9.9 - - - +
140F LEU* 4.2 4.7 - - + -
198F CYS* 4.3 4.3 - - - +
200F VAL* 3.9 36.8 - - + -
205F LEU* 5.7 0.2 - - + -
209F VAL* 4.3 16.3 - - + +
211F LYS* 2.8 50.0 + - + +
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Residues in contact with PHE 120 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118F SER* 3.3 38.1 - - - -
119F VAL* 1.3 81.9 - - - +
121F ILE* 1.3 59.9 + - - +
122F PHE* 4.4 9.4 - - + -
137F VAL 4.1 0.4 - - - +
138F CYS* 3.4 2.6 - - - -
139F LEU* 2.8 58.8 + - + +
141F ASN* 4.3 4.9 - - + -
211F LYS* 4.7 3.4 - - - -
140G GLU* 6.4 0.9 - - + -
142G THR* 3.7 23.6 - - + -
143G ALA* 4.3 1.6 - - - -
144G ALA* 3.5 39.9 - - + -
190G THR* 4.3 12.1 - - + -
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Residues in contact with ILE 121 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120F PHE* 1.3 73.1 - - - +
122F PHE* 1.3 72.9 + - - +
123F PRO* 4.4 2.9 - - - +
137F VAL 3.5 9.0 - - - +
138F CYS* 4.4 0.2 - - - +
152F TRP* 4.0 19.5 - - + -
196F TYR 3.8 11.9 - - - +
197F ALA* 4.0 7.6 - - - -
198F CYS* 4.2 5.8 - - - +
211F LYS* 3.5 39.4 - - + +
212F SER* 3.8 18.6 - - - +
213F PHE* 3.6 33.9 - - + -
133G PRO* 4.6 9.5 - - - +
134G CYS* 5.0 1.2 + - - +
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Residues in contact with PHE 122 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120F PHE* 4.4 8.5 - - + -
121F ILE* 1.3 78.6 - - - +
123F PRO* 1.3 70.9 - - + +
135F SER 4.5 0.3 - - - +
136F VAL* 3.4 6.6 - - - +
137F VAL* 2.7 57.6 + - + +
139F LEU* 4.3 20.0 - - + -
213F PHE* 4.1 4.0 - - - -
131G LEU* 3.6 33.0 - - + -
132G ALA* 3.3 34.5 - - - +
133G PRO* 4.0 2.5 - - + -
144G ALA* 3.3 45.8 - - + -
145G LEU* 4.3 5.6 - - - -
188G VAL* 4.5 11.7 - - + -
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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