Contacts of the strand formed by residues 118 - 123 (chain E) in PDB entry 4JRX
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 THR 118 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E GLN* 3.1 21.0 + - - +
7E THR 4.2 0.7 - - - -
8E PRO* 2.6 37.1 + - + +
9E LYS 3.5 1.6 - - - +
11E GLN* 4.8 2.2 - - + -
21E LEU* 3.6 38.3 - - + +
100E SER 3.5 0.7 - - - +
101E VAL* 3.3 3.7 - - - -
102E TYR* 2.8 37.6 + - - +
117E GLY* 1.3 69.0 - - - -
119E ARG* 1.3 67.2 + - - +
120E LEU* 3.5 16.2 + - + -
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Residues in contact with ARG 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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47D SER 5.4 4.9 + - - -
48D GLY* 4.0 24.0 + - - -
49D GLU* 5.7 2.2 - - - +
9E LYS* 2.8 39.4 + - - +
10E PHE* 3.3 37.3 - - + -
11E GLN 2.9 25.1 + - - -
100E SER 3.9 3.6 - - - -
101E VAL* 3.6 35.6 - - + +
103E PHE* 4.0 0.8 - - - -
116E GLN* 2.8 29.9 + - - +
117E GLY* 3.1 21.4 + - - -
118E THR* 1.3 69.4 - - - +
120E LEU* 1.3 59.4 + - - +
163E HIS* 3.5 18.7 - - + +
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Residues in contact with LEU 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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11E GLN* 3.3 15.0 - - + +
13E LEU* 4.2 22.4 - - + -
19E MET* 3.4 25.8 - - + -
21E LEU* 3.9 17.3 - - + -
91E LEU* 4.4 11.2 - - + -
98E GLN 4.5 2.2 - - - +
99E THR* 3.4 4.6 - - - +
100E SER 3.0 33.1 + - - +
102E TYR* 4.0 24.0 - - + -
118E THR* 3.5 4.7 + - + +
119E ARG* 1.3 72.9 - - - +
121E THR* 1.3 67.4 + - - +
122E VAL* 3.8 24.9 - - + -
163E HIS* 4.2 0.6 + - - -
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Residues in contact with THR 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 GLN 2.8 10.6 + - - -
12E VAL* 3.5 3.2 - - - +
13E LEU* 2.6 34.8 + - - +
99E THR* 3.8 17.3 - - + +
120E LEU* 1.3 73.9 + - - +
122E VAL* 1.3 58.6 + - - +
123E THR* 3.9 9.6 + - + -
160E TYR* 3.6 26.7 - - + +
161E PRO* 3.6 22.3 - - + +
162E ASP* 4.1 5.5 + - - +
163E HIS* 2.7 32.9 + - - -
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Residues in contact with VAL 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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13E LEU* 3.2 6.5 - - + +
14E LYS 4.2 0.4 - - - -
15E THR* 3.8 15.3 - - - -
94E ALA* 3.6 33.0 - - + +
95E ALA 3.4 37.9 - - - +
96E PRO* 4.0 13.0 - - + +
98E GLN* 4.1 5.2 - - + -
99E THR* 2.7 29.8 + - - +
120E LEU* 3.8 20.2 - - + -
121E THR* 1.3 72.6 - - - +
123E THR* 1.3 63.4 + - - +
160E TYR* 4.1 7.3 + - - -
194E ASP* 4.7 2.8 - - - +
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Residues in contact with THR 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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12E VAL* 4.0 20.3 - - + +
13E LEU 2.7 16.4 + - - -
14E LYS* 3.6 5.4 - - - -
15E THR* 2.7 33.9 + - - -
96E PRO* 5.6 1.1 - - - -
121E THR* 4.0 9.9 - - + -
122E VAL* 1.3 76.4 - - - +
124E GLU* 1.4 58.2 + - - +
125E ASP 3.4 22.2 + - - -
126E LEU* 4.2 8.3 + - - +
129E VAL* 4.2 6.1 - - + -
160E TYR* 3.4 32.8 - - + +
161E PRO* 5.6 0.7 - - + -
194E ASP* 4.1 5.2 - - - -
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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