Contacts of the strand formed by residues 116 - 122 (chain E) in PDB entry 1K9A
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 TYR 116 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83E PHE* 3.6 38.8 - + - -
106E VAL* 4.1 4.3 - - + -
107E ARG 3.2 13.7 - - - +
108E GLU* 4.3 10.1 - - + -
109E SER* 3.6 1.2 - - - +
114E GLY 3.8 7.2 - - - -
115E ASP* 1.3 83.3 - - - +
117E THR* 1.3 64.8 + - - +
130E ARG* 3.7 1.9 - - - +
131E ILE* 2.7 49.2 + - + +
133E TYR* 3.8 27.4 - + - -
138E LEU* 3.6 22.9 - - + -
149E LEU* 3.7 12.6 - - + -
228E ALA* 3.8 17.7 - - + +
229E THR* 3.8 10.0 + - - -
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Residues in contact with THR 117 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89E ARG* 5.1 0.2 - - - +
106E VAL* 3.4 4.2 - - - +
107E ARG* 2.9 65.4 + - - +
109E SER* 3.6 17.0 + - - -
110E THR* 3.9 8.3 + - - +
112E TYR* 6.1 0.3 - - - -
116E TYR* 1.3 79.8 + - - +
118E LEU* 1.3 66.0 + - - +
119E CYS* 3.8 8.7 + - - -
128E HIS* 4.0 6.5 - - + -
129E TYR 3.2 25.7 + - - +
130E ARG* 4.5 5.3 - - - +
131E ILE* 4.1 3.6 - - - -
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Residues in contact with LEU 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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104E PHE* 4.1 22.2 - - + -
105E LEU 3.9 1.3 - - - +
106E VAL* 3.8 22.4 - - + -
117E THR* 1.3 71.7 - - - +
119E CYS* 1.3 61.6 + - - +
120E VAL* 3.9 9.4 - - + -
127E GLU 3.4 2.6 - - - +
128E HIS* 3.5 1.2 - - - -
129E TYR* 2.7 47.7 + - + +
131E ILE* 3.9 15.5 - - + +
140E ILE* 4.2 14.1 - - + -
152E LEU* 4.4 13.9 - - + -
153E VAL* 5.0 0.7 - - + -
156E TYR* 4.9 0.2 - - + -
163E LEU* 3.8 31.2 - - + -
167E LEU* 4.2 18.6 - - + -
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Residues in contact with CYS 119 (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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92E ALA* 4.2 1.6 - - + -
96E LEU* 3.8 22.1 - - + +
104E PHE* 3.0 27.4 - - - +
105E LEU* 3.0 22.2 + - + +
107E ARG* 3.3 34.3 - - - -
117E THR* 3.8 11.0 - - - -
118E LEU* 1.3 78.0 - - - +
120E VAL* 1.3 61.6 + - - +
126E VAL* 4.9 0.4 - - + -
127E GLU 3.1 7.2 - - - +
128E HIS* 3.3 22.4 - - + +
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Residues in contact with VAL 120 (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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96E LEU* 4.9 2.0 - - - -
102E GLY* 4.2 8.1 - - - -
103E LEU 3.1 17.5 - - - +
104E PHE* 4.0 1.6 - - + -
118E LEU* 3.9 16.4 - - + -
119E CYS* 1.3 79.0 - - - +
121E SER* 1.3 62.9 + - - +
122E CYS* 4.4 2.2 - - - -
126E VAL* 3.5 5.0 - - - -
127E GLU* 2.6 41.8 + - + +
129E TYR* 4.1 20.2 - - + -
163E LEU* 5.1 2.7 - - + -
164E CYS* 5.1 0.2 - - - -
165E THR* 3.8 29.4 - - + +
167E LEU* 3.9 24.0 - - + -
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Residues in contact with SER 121 (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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96E LEU* 3.9 19.5 + - - +
99E PRO* 3.7 11.4 - - - +
100E GLU 2.9 46.1 + - - +
101E THR* 3.4 12.2 - - - +
102E GLY 3.7 4.5 + - - -
103E LEU* 3.1 18.5 + - - -
120E VAL* 1.3 70.9 - - - +
122E CYS* 1.3 63.4 + - - +
124E GLY* 4.7 4.7 + - - -
125E LYS 3.4 9.9 + - - -
126E VAL* 4.5 3.2 - - - +
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Residues in contact with CYS 122 (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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101E THR* 5.1 1.8 - - - -
120E VAL* 3.7 4.2 + - - -
121E SER* 1.3 73.4 - - - +
123E GLU* 1.3 69.7 + - - +
124E GLY 3.0 2.0 - - - -
125E LYS* 2.5 44.8 + - + +
127E GLU* 3.8 11.7 - - + -
164E CYS* 2.0 53.8 - - + -
165E THR* 3.2 29.6 - - - -
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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