Contacts of the helix formed by residues 113 - 124 (chain E) in PDB entry 4DVQ
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 LEU 113 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111E MET 3.2 4.9 + - - +
112E ILE* 1.3 75.3 - - - +
114E GLU* 1.3 63.1 + - - +
115E PRO* 4.2 6.5 - - + -
116E TRP* 3.3 39.3 + - + +
117E VAL* 3.1 24.6 + - - +
130E PHE* 4.2 12.6 - - + -
131E LEU* 4.4 12.1 - - + +
234E THR* 4.2 4.5 - - + -
238E MET* 4.0 30.5 - - + -
487E PHE* 3.3 37.2 - - + -
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Residues in contact with GLU 114 (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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112E ILE* 3.4 24.5 + - + +
113E LEU* 1.3 68.8 - - - +
115E PRO* 1.3 65.4 - - + +
117E VAL* 4.1 2.0 - - - +
118E ALA* 2.7 38.2 + - - +
237E LEU 5.9 1.6 - - - +
240E MET 4.5 3.5 - - - +
241E PRO* 4.0 7.6 - - - +
242E ARG* 3.4 43.4 + - + +
253E TRP* 4.7 5.8 - - + -
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Residues in contact with PRO 115 (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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113E LEU* 3.3 14.8 - - + -
114E GLU* 1.3 94.5 - - + +
116E TRP* 1.3 66.1 + - + +
118E ALA* 3.4 2.9 - - - +
119E TYR* 3.1 21.7 + - - +
234E THR* 4.6 8.1 - - + +
237E LEU* 3.8 37.7 - - + +
238E MET* 4.4 7.4 - - - +
253E TRP* 3.8 14.1 - - + -
256E HIS* 3.4 33.6 - - + +
257E PHE* 4.1 1.6 - - - -
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Residues in contact with TRP 116 (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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113E LEU* 3.3 27.6 + - + +
115E PRO* 1.3 81.4 - - + +
117E VAL* 1.3 61.8 + - - +
119E TYR* 3.2 9.5 + - - +
120E ARG* 3.1 33.7 + - - +
130E PHE* 3.8 22.2 - + - -
131E LEU* 3.7 18.8 - - + -
230E MET* 3.4 29.4 - - + -
231E PHE* 4.1 2.0 - + - -
234E THR* 2.8 30.4 + - + +
256E HIS* 3.7 10.8 - - - -
260E TRP* 3.4 23.6 - + - +
310E GLU* 6.0 0.2 - - - -
487E PHE* 3.8 26.5 - + - -
602E 1CA 3.6 45.1 - - + -
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Residues in contact with VAL 117 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112E ILE* 4.0 22.7 - - + -
113E LEU 3.1 18.1 + - - +
114E GLU* 4.1 2.5 - - - +
116E TRP* 1.3 71.9 - - - +
118E ALA* 1.3 67.1 + - - +
119E TYR 3.3 0.2 + - - -
120E ARG* 3.3 4.9 + - - +
121E GLN* 3.1 36.4 + - + +
127E CYS* 4.2 14.6 - - - -
131E LEU* 4.1 36.3 - - + +
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Residues in contact with ALA 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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114E GLU 2.7 23.7 + - - +
115E PRO 3.4 6.5 - - - +
116E TRP 3.3 0.2 - - - -
117E VAL* 1.3 72.0 - - - +
119E TYR* 1.3 62.7 + - - +
121E GLN* 3.2 15.3 + - - +
122E HIS* 2.9 26.0 + - - +
242E ARG* 3.5 26.8 + - - +
253E TRP* 3.8 17.0 - - + -
257E PHE* 4.0 4.7 - - + -
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Residues in contact with TYR 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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115E PRO 3.1 11.8 + - - +
116E TRP 3.6 8.7 - - - +
117E VAL 3.2 0.8 - - - -
118E ALA* 1.3 76.1 - - - +
120E ARG* 1.3 69.4 + - - +
122E HIS* 2.9 13.2 + - - +
123E ARG* 3.1 37.5 + - + +
125E HIS* 4.5 3.1 + + - -
257E PHE* 3.7 34.7 - + + -
260E TRP* 3.6 39.1 + + + -
261E ASP* 2.3 42.9 + - - -
264E PHE* 3.5 48.4 - + - +
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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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116E TRP* 3.1 29.4 + - - +
117E VAL 3.3 5.1 + - - +
119E TYR* 1.3 80.9 - - - +
121E GLN* 1.3 57.0 + - - +
123E ARG 3.4 0.5 + - - -
124E GLY 3.0 8.5 + - - -
125E HIS* 2.8 49.0 + - - +
126E LYS 4.2 10.0 + - - +
127E CYS* 3.6 29.6 - - - +
131E LEU* 3.6 19.5 - - + +
260E TRP* 3.5 50.1 - - - +
264E PHE* 3.7 30.8 - - - -
309E MET* 5.8 3.0 - - - +
310E GLU* 4.6 17.2 + - - +
602E 1CA 4.7 1.4 + - - -
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Residues in contact with GLN 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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117E VAL* 3.1 34.7 + - + +
118E ALA* 3.2 23.2 - - - +
120E ARG* 1.3 76.7 - - - +
122E HIS* 1.3 61.7 + - + +
123E ARG 3.4 0.5 + - - -
124E GLY* 3.5 10.0 + - - -
125E HIS 5.0 0.9 - - - -
242E ARG* 4.4 12.6 - - - +
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Residues in contact with HIS 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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118E ALA 2.9 18.1 + - - +
119E TYR 2.9 5.1 + - - +
121E GLN* 1.3 78.8 - - + +
123E ARG* 1.3 88.6 + - + +
242E ARG* 6.1 1.5 + - - +
257E PHE* 3.7 33.0 - + + -
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Residues in contact with ARG 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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119E TYR* 3.1 34.3 + - + +
122E HIS* 1.3 101.5 + - + +
124E GLY* 1.3 61.7 + - - +
125E HIS* 3.4 34.5 + - + +
257E PHE* 5.5 4.6 - - - +
261E ASP* 2.7 38.5 + - - -
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Residues in contact with GLY 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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120E ARG 3.0 4.7 + - - -
121E GLN* 3.5 10.2 + - - -
122E HIS 3.5 0.2 - - - -
123E ARG* 1.3 79.3 - - - +
125E HIS* 1.3 63.5 + - - +
126E LYS 4.0 0.5 + - - -
302E GLU* 5.3 2.8 - - - +
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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