Contacts of the strand formed by residues 113 - 117 (chain Y) in PDB entry 3HI6
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 113 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111Y ALA 3.9 1.4 + - - -
112Y PRO* 1.3 73.1 - - - +
114Y VAL* 1.3 61.4 + - - +
115Y PHE* 3.8 22.6 - - - -
134Y LEU 3.4 3.3 - - - +
135Y LEU* 3.4 0.7 - - - -
136Y ASN* 2.8 41.4 + - - +
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Residues in contact with VAL 114 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112Y PRO* 4.4 9.2 - - + +
113Y SER* 1.3 76.9 - - - +
115Y PHE* 1.3 76.8 + - - +
133Y CYS* 3.8 15.0 - - - -
134Y LEU 3.2 7.9 - - - +
135Y LEU* 4.3 6.3 - - + -
193Y CYS* 4.4 1.3 - - - +
195Y VAL* 3.5 44.9 - - + -
204Y VAL* 4.1 18.8 - - + +
206Y LYS* 3.5 45.5 + - + +
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Residues in contact with PHE 115 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142X THR* 4.3 19.5 - - - -
143X ALA* 4.7 0.9 - - - -
144X ALA* 3.6 34.1 - - + -
190X THR* 4.6 9.4 - - + -
113Y SER* 3.8 34.1 - - - -
114Y VAL* 1.3 82.9 - - - +
116Y ILE* 1.3 60.0 - - - +
117Y PHE* 4.0 20.2 - - + -
132Y VAL 3.8 0.5 - - - +
133Y CYS* 3.4 5.5 - - - -
134Y LEU* 2.8 48.0 + - + +
136Y ASN* 4.3 10.8 - - + -
206Y LYS* 4.5 3.6 - - - -
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Residues in contact with ILE 116 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132X ALA 5.2 0.2 - - - +
115Y PHE* 1.3 74.5 - - - +
117Y PHE* 1.3 73.6 + - - +
118Y PRO* 4.2 3.7 - - + +
131Y VAL* 4.4 4.9 - - + -
132Y VAL 3.4 8.3 - - - +
147Y TRP* 4.0 13.7 - - + -
191Y TYR 3.5 20.0 - - - +
193Y CYS* 4.0 16.6 - - - +
206Y LYS* 3.4 30.3 - - + +
207Y SER 4.0 20.6 - - - +
208Y PHE* 3.8 30.5 - - + -
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Residues in contact with PHE 117 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131X LEU* 3.5 45.9 - - + +
132X ALA 3.1 30.1 - - - +
133X PRO* 4.6 0.7 - - + -
144X ALA* 3.5 36.3 - - + -
145X LEU* 4.0 6.7 - - - -
188X VAL* 4.9 5.8 - - + -
115Y PHE* 4.0 19.7 - - + -
116Y ILE* 1.3 80.8 - - - +
118Y PRO* 1.3 69.8 - - + +
130Y SER 4.4 0.2 - - - +
131Y VAL* 3.4 8.8 - - - +
132Y VAL* 2.8 48.3 + - + +
134Y LEU* 4.2 17.3 - - + -
208Y PHE* 4.3 1.1 - - - -
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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