Contacts of the strand formed by residues 114 - 118 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112E ALA 4.7 2.1 + - - -
113E PRO* 1.3 75.5 + - - +
115E VAL* 1.3 63.4 + - - +
116E PHE* 3.7 26.0 + - - -
135E LEU 3.0 13.3 - - - +
136E LEU* 3.5 0.3 - - - -
137E ASN* 3.0 30.3 + - - +
138E ASN* 5.7 0.2 + - - -
141F THR* 5.5 3.4 - - - -
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Residues in contact with VAL 115 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113E PRO* 4.1 7.6 + - + +
114E SER* 1.3 77.8 - - - +
116E PHE* 1.3 71.5 + - - +
134E CYS* 3.9 24.2 - - - -
135E LEU 3.3 2.9 - - - +
136E LEU* 4.6 6.3 - - + -
194E CYS* 4.7 1.3 - - - +
196E VAL* 3.8 33.7 - - + -
201E LEU* 5.7 1.8 - - + -
205E VAL* 4.1 19.3 - - + -
207E LYS* 3.3 50.2 - - + +
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Residues in contact with PHE 116 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114E SER* 3.9 29.6 - - - -
115E VAL* 1.3 83.5 - - - +
117E ILE* 1.3 61.1 + - - +
118E PHE* 4.2 21.8 - + + -
133E VAL 3.6 1.2 - - - +
134E CYS* 3.3 6.1 - - - -
135E LEU* 2.8 49.5 + - + +
137E ASN* 4.8 2.2 - - + -
207E LYS* 4.7 1.3 - - - -
132F PRO* 6.1 5.8 - - + -
139F GLU* 6.5 0.9 - - + -
141F THR* 4.0 30.1 - - - -
142F ALA* 4.0 2.9 - - - -
143F ALA* 3.8 40.4 - - + -
189F THR* 4.7 11.0 - - + -
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Residues in contact with ILE 117 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116E PHE* 1.3 74.7 - - - +
118E PHE* 1.3 73.2 + - - +
119E PRO* 4.2 2.1 - - + +
133E VAL 3.5 7.0 - - - +
134E CYS* 4.6 0.4 - - - +
148E TRP* 3.8 31.0 - - + -
192E TYR 4.2 9.6 - - - +
194E CYS* 4.2 7.2 - - + +
207E LYS* 3.9 37.1 - - + +
208E SER 4.2 17.0 - - - +
209E PHE* 3.7 34.5 - - + -
132F PRO* 4.0 14.9 - - - +
133F CYS 5.0 0.5 + - - -
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Residues in contact with PHE 118 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116E PHE* 4.2 19.3 - + + -
117E ILE* 1.3 80.0 - - - +
119E PRO* 1.3 68.9 - - - +
132E VAL* 3.7 5.0 - - - +
133E VAL* 2.7 51.6 + - + +
135E LEU* 4.2 18.8 - - + -
130F LEU* 4.0 33.9 - - + -
131F ALA 3.7 10.3 - - - -
132F PRO* 3.4 44.6 - - + -
143F ALA* 3.2 30.5 - - + -
144F LEU* 3.9 6.1 - - - -
187F VAL* 4.9 4.7 - - + -
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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