Contacts of the strand formed by residues 136 - 139 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94A THR* 3.2 19.7 - - + +
95A GLY* 4.0 5.4 - - - -
118A PHE* 3.8 26.2 - - + -
122A ILE* 4.1 6.7 - - + -
135A PHE* 1.3 83.5 - - - +
137A KCX 1.3 66.5 + - - +
156A ALA* 3.8 24.2 - - + +
159A ALA* 4.2 15.0 - - + -
160A ASN 5.2 0.4 - - - +
165A VAL* 3.9 17.9 - - + -
166A PRO 3.0 8.7 + - - +
167A ILE* 3.3 9.2 - - + +
168A ILE 2.8 26.5 + - - +
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Residues in contact with KCX 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A HIS* 3.0 24.1 + - - -
24A HIS* 2.8 35.2 + - - -
67A PRO* 3.5 29.1 + - + +
69A VAL* 3.8 28.5 - - + -
72A LEU* 3.7 5.5 - - - +
94A THR 2.8 6.4 + - - +
95A GLY* 3.4 2.1 - - - -
96A ILE 3.2 24.5 + - - +
97A TYR* 3.8 21.4 - - + -
135A PHE* 4.3 10.3 - - + -
136A VAL* 1.3 74.4 - - - +
138A ILE* 1.3 72.5 + - - +
168A ILE* 3.2 23.1 - - + +
169A THR 4.0 1.8 - - - -
170A HIS* 3.1 44.5 + - - +
199A HIS* 3.1 4.7 + - - -
256A ASP* 4.0 1.0 + - - -
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Residues in contact with ILE 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A ILE 3.7 7.2 - - - -
97A TYR* 5.5 0.2 - - - -
118A PHE* 5.2 0.2 - - + -
136A VAL* 4.4 3.1 - - + -
137A KCX 1.3 85.4 - - - +
139A ALA* 1.4 63.8 + - - +
152A VAL* 3.7 25.6 - - + +
153A ILE* 4.0 29.4 - - + -
156A ALA* 3.7 22.9 - - + -
167A ILE* 4.1 13.2 - - + -
168A ILE 3.1 3.7 + - - +
169A THR* 3.2 32.3 - - + -
170A HIS 2.8 22.9 + - - -
181A GLN* 4.5 6.5 - - + +
185A LEU* 4.1 13.9 - - + -
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Residues in contact with ALA 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A ILE 4.1 4.2 + - - -
97A TYR* 3.7 27.1 - - + -
98A ILE* 3.5 23.2 + - - +
99A TYR* 4.4 1.3 - - + -
138A ILE* 1.4 78.9 - - - +
140A ALA* 1.3 64.7 + - - +
149A VAL* 3.4 17.0 - - - +
152A VAL* 5.3 2.3 - - - +
153A ILE* 5.4 1.6 - - - +
170A HIS* 3.4 27.6 - - + -
181A GLN* 3.7 3.8 + - - +
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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