Contacts of the strand formed by residues 136 - 139 (chain C) in PDB entry 4KEU
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 VAL 136 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C THR* 3.2 21.5 - - + +
95C GLY* 4.1 2.5 - - - -
118C PHE* 3.8 19.5 - - + -
122C ILE* 4.0 7.2 - - + -
135C PHE* 1.3 79.0 - - - +
137C KCX 1.3 64.9 + - - +
138C ILE* 4.3 0.9 - - + -
156C ALA* 3.7 27.4 - - + +
159C ALA* 4.0 16.6 - - + -
160C ASN 5.1 0.7 - - - +
165C VAL* 3.9 17.3 - - + -
166C PRO 2.9 10.2 + - - +
167C ILE* 3.3 14.1 - - + +
168C ILE 2.9 28.1 + - - +
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Residues in contact with KCX 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C HIS* 3.0 18.2 + - - -
24C HIS* 2.8 35.7 + - - -
67C PRO* 3.6 24.9 + - + +
69C VAL* 3.8 28.3 - - + -
72C LEU* 3.8 4.3 - - - +
94C THR 2.7 9.9 + - - +
95C GLY* 3.3 3.3 - - - -
96C ILE 3.2 24.9 + - - +
97C TYR* 3.9 20.9 - - + -
135C PHE* 4.1 13.2 - - + -
136C VAL* 1.3 71.5 - - - +
138C ILE* 1.4 80.8 + - - +
168C ILE* 3.2 24.7 - - + +
169C THR 4.0 1.6 - - - -
170C HIS* 3.1 36.7 + - - +
199C HIS* 3.1 13.9 + - - -
256C ASP* 3.9 1.4 + - - -
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Residues in contact with ILE 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C ILE 3.7 6.7 - - - -
118C PHE* 5.2 0.7 - - + -
136C VAL* 4.3 3.1 - - + -
137C KCX 1.4 85.4 - - - +
139C ALA* 1.3 64.2 + - - +
152C VAL* 3.7 23.6 - - + +
153C ILE* 3.8 35.0 - - + -
156C ALA* 3.6 26.5 - - + -
167C ILE* 4.3 5.8 - - + -
168C ILE 3.1 2.7 + - - +
169C THR* 3.2 31.4 - - + -
170C HIS 2.8 23.6 + - - -
181C GLN* 4.7 7.9 - - + +
185C LEU* 4.3 12.1 - - + -
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Residues in contact with ALA 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96C ILE 4.0 4.0 + - - -
97C TYR* 3.6 35.7 - - + -
98C ILE* 3.6 24.4 + - - +
99C TYR* 4.5 1.3 - - + -
138C ILE* 1.3 80.8 - - - +
140C ALA* 1.3 66.0 + - - +
149C VAL* 3.5 18.0 - - - +
152C VAL* 5.3 2.2 - - - +
153C ILE* 5.3 1.9 - - - +
170C HIS* 3.4 16.4 - - + -
181C GLN* 3.7 3.1 + - - +
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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
------------------------------------------------------------
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