Contacts of the strand formed by residues 119 - 124 (chain E) in PDB entry 4PRH
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 119 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6E GLN* 4.1 7.4 + - - +
7E THR 4.1 12.3 + - - -
8E PRO 2.7 22.3 + - - -
9E LYS 3.7 4.7 - - - -
11E LEU* 4.2 1.8 - - - -
21E LEU* 4.1 31.6 - - - +
22E ARG 5.3 0.3 + - - -
100E ALA 3.5 0.3 - - - +
101E LEU* 3.5 2.8 - - - +
102E TYR* 2.8 39.0 + - - +
118E GLY* 1.4 71.9 + - - -
120E ARG* 1.3 61.1 + - - +
121E LEU 3.5 3.9 + - - -
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Residues in contact with ARG 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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9E LYS 2.9 16.7 + - - +
10E HIS* 3.5 15.1 - - + +
11E LEU* 3.0 28.9 + - - +
46E LEU* 5.1 12.7 - - - +
100E ALA 3.7 9.4 - - - +
101E LEU* 4.3 20.8 - - + +
118E GLY 4.1 0.6 - - - -
119E SER* 1.3 68.6 - - - +
121E LEU* 1.3 61.8 + - - +
122E THR* 4.5 5.7 + - - -
163E ASP* 3.0 49.1 + - - +
164E HIS* 3.5 43.4 + - + +
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Residues in contact with LEU 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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11E LEU* 3.6 25.6 - - + +
13E THR* 3.3 26.7 - - - +
19E VAL* 4.1 11.0 - - + -
21E LEU* 5.6 0.7 - - + -
91E LEU* 3.8 28.7 - - + -
94E LEU* 3.9 18.2 - - + -
98E ASP 3.9 15.3 - - - +
99E SER* 3.3 4.7 - - - -
100E ALA 3.0 25.2 + - - +
102E TYR* 3.9 16.8 - - + -
119E SER 3.5 1.2 + - - -
120E ARG* 1.3 76.0 + - - +
122E THR* 1.3 68.7 + - - +
123E VAL* 3.8 12.6 - - + -
164E HIS* 4.7 0.2 - - - -
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Residues in contact with THR 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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11E LEU 3.0 9.2 + - - -
12E ILE* 3.3 5.4 - - + -
13E THR* 3.0 27.2 + - - +
99E SER* 4.1 4.5 - - - -
120E ARG* 4.0 7.3 + - - -
121E LEU* 1.3 72.6 + - - +
123E VAL* 1.3 61.8 - - - +
124E LEU* 3.7 28.7 - - + -
162E PRO* 3.7 22.9 - - + +
164E HIS* 2.8 30.9 - - - -
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Residues in contact with VAL 123 (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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13E THR* 3.4 3.8 - - - +
14E ALA 3.9 16.2 - - - +
15E THR* 3.8 23.6 - - + -
94E LEU* 4.0 18.6 - - + -
95E GLU 3.7 26.0 - - - +
96E LEU* 3.2 14.7 - - - +
99E SER* 3.2 24.0 + - - +
121E LEU* 3.8 29.8 - - + -
122E THR* 1.3 75.3 - - - +
124E LEU* 1.3 67.4 + - - +
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Residues in contact with LEU 124 (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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12E ILE* 3.9 17.7 - - + -
13E THR 2.8 9.9 + - - +
14E ALA* 3.0 7.6 - - - -
15E THR* 2.9 27.8 + - - -
96E LEU* 3.9 3.1 - - + -
122E THR* 3.7 23.8 - - + -
123E VAL* 1.3 76.7 - - - +
125E GLU* 1.3 59.7 + - - +
126E ASP 3.5 15.0 - - - +
127E LEU* 4.1 5.2 - - + -
130E VAL* 3.6 31.6 - - + -
161E TYR* 3.6 35.7 - - + +
162E PRO* 4.2 4.5 - - + -
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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