Contacts of the strand formed by residues 114 - 118 (chain O) in PDB entry 3KYM
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 114 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112O ALA 3.5 2.6 + - - -
113O PRO* 1.3 72.3 - - - +
115O VAL* 1.3 59.0 + - - +
116O PHE* 3.2 32.8 - - - -
135O LEU 3.4 0.5 - - - +
137O ASN* 3.1 32.8 + - - +
141P THR* 5.1 2.9 - - - +
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Residues in contact with VAL 115 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113O PRO* 3.9 8.5 + - + +
114O SER* 1.3 70.8 - - - +
116O PHE* 1.3 81.2 + - - +
134O CYS* 3.7 26.9 - - - -
135O LEU 3.4 6.3 - - - +
136O LEU* 4.5 8.3 - - + -
194O CYS* 4.8 2.5 - - + +
196O VAL* 3.8 34.1 - - + -
201O LEU* 5.4 0.4 - - + -
205O VAL* 3.9 19.5 - - + +
207O LYS* 3.8 42.1 - - + +
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Residues in contact with PHE 116 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114O SER* 3.2 31.6 - - - -
115O VAL* 1.3 85.8 - - - +
117O ILE* 1.3 61.8 + - - +
118O PHE* 4.2 18.8 - - + -
133O VAL 3.9 0.4 - - - +
134O CYS* 3.3 6.1 - - - -
135O LEU* 2.8 56.3 + - + +
137O ASN* 4.0 12.3 - - + -
207O LYS* 5.1 4.0 - - - -
132P PRO* 6.3 3.6 - - + -
141P THR* 3.8 33.2 - - + -
142P ALA* 5.5 0.2 - - - -
143P ALA* 3.7 27.4 - - + -
189P THR* 4.4 6.3 - - + -
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Residues in contact with ILE 117 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116O PHE* 1.3 76.0 - - - +
118O PHE* 1.3 70.2 + - - +
119O PRO* 3.9 6.4 - - - +
132O VAL* 4.3 1.3 - - + -
133O VAL 3.4 8.7 - - - +
148O TRP* 3.5 34.3 - - + -
192O TYR 4.0 11.9 - - - +
194O CYS* 4.0 19.1 - - + +
207O LYS* 4.0 25.7 - - + +
208O SER* 4.0 11.7 - - - +
209O PHE* 3.7 31.6 - - + -
132P PRO* 4.2 11.4 - - - +
133P CYS* 5.1 3.3 + - - -
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Residues in contact with PHE 118 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116O PHE* 4.2 11.2 - - + -
117O ILE* 1.3 76.6 - - - +
119O PRO* 1.3 70.4 - - + +
131O SER 4.2 0.3 - - - +
132O VAL* 3.4 8.4 - - - +
133O VAL* 2.7 54.0 + - + +
135O LEU* 3.9 27.4 - - + -
209O PHE* 4.5 0.2 - - - -
130P LEU* 3.6 35.5 - - + +
131P ALA 3.5 22.9 - - - +
132P PRO* 3.8 8.1 - - + -
143P ALA* 3.4 42.6 - - + -
144P LEU* 3.8 15.5 - - - -
187P VAL* 4.9 2.2 - - + -
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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