Contacts of the strand formed by residues 114 - 118 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112I ALA 3.5 4.0 + - - -
113I PRO* 1.3 70.7 - - - +
115I VAL* 1.3 57.8 + - - +
116I PHE* 3.2 25.7 - - - -
135I LEU 3.2 4.2 - - - +
137I ASN* 3.0 47.3 + - - +
141J THR* 4.5 15.0 - - - +
189J THR* 4.9 0.3 + - - -
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Residues in contact with VAL 115 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113I PRO* 3.5 14.6 - - + +
114I SER* 1.3 69.9 - - - +
116I PHE* 1.3 74.9 + - - +
134I CYS* 3.8 17.5 - - - -
135I LEU 3.1 3.8 - - - -
136I LEU* 3.4 30.3 - - + -
194I CYS* 4.6 1.3 - - + +
196I VAL* 3.9 20.2 - - + -
205I VAL* 4.7 20.6 - - + +
207I LYS* 3.3 45.0 + - + +
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Residues in contact with PHE 116 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114I SER* 3.2 42.2 - - - -
115I VAL* 1.3 93.0 - - - +
117I ILE* 1.3 59.3 + - - +
118I PHE* 4.0 20.2 - + + -
134I CYS* 3.2 10.6 - - - -
135I LEU* 2.7 43.0 + - + -
137I ASN* 4.7 3.1 - - + -
207I LYS* 4.4 11.7 - - - +
132J PRO* 6.0 5.4 - - + -
141J THR* 3.7 21.5 - - + -
142J ALA* 3.8 9.9 - - + -
143J ALA* 3.5 44.6 - - + -
189J THR* 4.8 2.9 - - - -
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Residues in contact with ILE 117 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116I PHE* 1.3 76.1 - - - +
118I PHE* 1.3 68.2 + - - +
119I PRO* 3.8 8.6 - - + +
132I VAL* 4.0 24.7 - - + -
133I VAL 3.5 7.2 - - - +
148I TRP* 4.2 14.4 - - + -
192I TYR* 3.3 31.4 - - + +
193I ALA* 4.4 3.4 - - - +
194I CYS* 4.4 7.9 - - + +
207I LYS* 4.2 12.6 - - + +
208I SER* 3.8 32.3 - - - +
209I PHE* 4.5 4.7 - - + +
132J PRO* 4.4 10.9 - - - +
133J CYS* 5.2 3.4 + - - -
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Residues in contact with PHE 118 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116I PHE* 4.0 20.2 - + + -
117I ILE* 1.3 73.8 - - - +
119I PRO* 1.3 68.0 - - + +
131I SER 4.1 0.7 - - - +
132I VAL* 3.5 6.9 - - - +
133I VAL* 2.8 59.0 + - + +
135I LEU* 3.7 33.9 - - + -
130J LEU* 3.6 26.5 - - + +
131J ALA* 3.4 30.5 - - - +
132J PRO* 4.2 2.0 - - + -
143J ALA* 3.4 28.7 - - + -
144J LEU* 4.1 9.2 - - - -
187J VAL* 4.5 14.1 - - + -
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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