Contacts of the strand formed by residues 115 - 119 (chain D) in PDB entry 4YHP
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 115 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143C THR* 6.0 1.6 - - - -
113D ALA 3.7 2.0 + - - -
114D PRO* 1.3 71.8 - - - +
116D VAL* 1.3 59.8 + - - +
117D PHE* 3.6 25.0 - - - -
136D LEU 3.3 3.3 - - - +
137D LEU* 3.5 1.6 - - - -
138D ASN* 2.9 43.6 + - - +
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Residues in contact with VAL 116 (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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114D PRO* 3.8 21.1 - - + +
115D SER* 1.3 78.5 - - - +
117D PHE* 1.3 70.9 + - - +
135D CYS* 3.8 17.9 - - - -
136D LEU 3.3 4.0 - - - +
137D LEU* 4.6 1.8 - - + -
195D CYS* 4.6 0.9 - - + -
197D VAL* 3.5 39.0 - - + -
202D LEU* 5.6 0.2 - - + -
206D VAL* 4.5 16.8 - - + -
208D LYS* 3.4 45.5 + - + +
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Residues in contact with PHE 117 (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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135C SER* 6.0 6.3 - - - -
143C THR* 3.9 20.9 - - - -
144C ALA* 4.5 1.8 - - - -
145C ALA* 3.5 43.3 - - + -
191C THR* 4.6 7.9 - - + -
115D SER* 3.6 34.5 - - - -
116D VAL* 1.3 81.0 - - - +
118D ILE* 1.3 61.2 + - - +
119D PHE* 4.0 20.2 - - + -
134D VAL 3.9 0.3 - - - +
135D CYS* 3.3 7.7 - - - -
136D LEU* 2.7 52.4 + - + +
138D ASN* 4.4 5.4 - - + -
208D LYS* 4.8 1.8 - - - -
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Residues in contact with ILE 118 (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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133C ALA 5.5 0.3 - - - +
135C SER* 5.5 4.7 - - - -
137C LYS* 5.1 11.9 + - - +
117D PHE* 1.3 75.2 - - - +
119D PHE* 1.3 69.8 + - - +
120D PRO* 3.9 6.2 - - - +
133D VAL* 4.5 3.8 - - + -
134D VAL 3.5 6.7 - - - +
135D CYS* 4.5 0.2 - - - +
149D TRP* 4.1 14.8 - - + -
193D TYR 3.4 25.4 - - - +
195D CYS* 3.7 15.3 - - + +
208D LYS* 3.6 25.6 - - + +
209D SER 3.7 28.0 - - - +
210D PHE* 3.7 25.4 - - + -
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Residues in contact with PHE 119 (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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132C LEU* 3.4 60.6 - - + -
133C ALA 3.2 28.7 - - - -
134C PRO* 4.8 0.2 - - + -
135C SER 5.3 1.3 - - - -
145C ALA* 3.2 33.7 - - + -
146C LEU* 3.9 5.4 - - - -
189C VAL* 5.0 2.7 - - + -
117D PHE* 4.0 21.1 - + + -
118D ILE* 1.3 79.8 - - - +
120D PRO* 1.3 68.3 - - + +
132D SER 4.4 0.5 - - - +
133D VAL* 3.4 8.1 - - - +
134D VAL* 2.7 44.5 + - + +
136D LEU* 4.3 15.3 - - + -
210D PHE* 4.2 2.9 - - - -
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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