Contacts of the helix formed by residues 113 - 124 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111I MET 3.1 9.3 + - - +
112I ILE* 1.3 66.7 - - - +
114I GLU* 1.3 65.2 + - - +
115I PRO* 3.5 10.0 - - + -
116I TRP* 3.3 52.7 - - + +
117I VAL* 3.1 28.4 + - - +
130I PHE* 4.3 8.7 - - + -
131I LEU* 4.0 13.2 - - + +
234I THR* 4.6 2.0 - - + -
238I MET* 4.3 21.3 - - + -
487I PHE* 3.7 29.6 - - + -
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Residues in contact with GLU 114 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112I ILE* 2.9 23.8 + - + +
113I LEU* 1.3 71.4 - - - +
115I PRO* 1.3 61.9 - - + +
117I VAL 3.5 0.7 + - - -
118I ALA* 2.8 37.1 + - - +
237I LEU 5.9 1.6 - - - +
238I MET* 5.5 2.0 - - - +
240I MET 4.0 10.7 - - - +
241I PRO* 4.0 5.2 - - - +
242I ARG* 3.4 64.5 + - + +
253I TRP* 4.7 3.1 - - + -
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Residues in contact with PRO 115 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113I LEU* 3.3 17.5 - - + -
114I GLU* 1.3 92.4 - - + +
116I TRP* 1.3 67.2 + - + +
118I ALA* 3.1 3.8 + - - +
119I TYR* 3.0 19.4 + - - +
234I THR* 4.5 6.1 - - + +
237I LEU* 3.9 36.3 - - + +
238I MET* 4.3 10.1 - - + +
253I TRP* 3.9 14.5 - - + -
256I HIS* 3.5 34.6 + - + +
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Residues in contact with TRP 116 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113I LEU* 3.3 30.8 + - + +
114I GLU 3.5 0.2 - - - -
115I PRO* 1.3 80.5 - - + +
117I VAL* 1.3 65.0 + - - +
119I TYR* 3.1 10.9 + - - +
120I ARG* 3.1 36.1 + - - +
130I PHE* 3.8 26.0 - + - -
131I LEU* 3.6 14.1 - - + -
230I MET* 3.5 31.0 - - + -
234I THR* 3.0 26.0 + - + +
256I HIS* 3.9 10.8 - + - -
260I TRP* 3.6 20.9 - + - +
310I GLU* 6.1 0.4 - - - -
487I PHE* 3.4 31.0 - + - -
602I 1CA 3.6 41.3 - - + -
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Residues in contact with VAL 117 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112I ILE* 4.2 17.0 - - + -
113I LEU 3.1 19.3 + - - +
114I GLU 4.0 2.5 - - - +
116I TRP* 1.3 79.0 - - - +
118I ALA* 1.3 62.3 + - - +
120I ARG* 3.1 9.8 + - - +
121I GLN* 3.0 38.0 + - + +
127I CYS* 4.2 15.0 - - - -
131I LEU* 4.0 33.7 - - + +
242I ARG* 4.2 11.4 - - - +
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Residues in contact with ALA 118 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114I GLU 2.8 18.8 + - - +
115I PRO 3.1 6.7 + - - +
117I VAL* 1.3 74.2 - - - +
119I TYR* 1.3 60.2 + - - +
121I GLN* 3.4 5.6 + - - +
122I HIS* 2.8 42.5 + - + +
242I ARG* 3.5 20.6 - - - +
253I TRP* 3.4 26.0 - - + -
257I PHE* 3.9 4.3 - - + -
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Residues in contact with TYR 119 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115I PRO 3.0 10.9 + - - +
116I TRP 3.1 8.0 + - - +
118I ALA* 1.3 75.3 - - - +
120I ARG* 1.3 70.3 + - - +
122I HIS 3.4 0.3 + - - -
123I ARG* 3.1 55.8 + - + +
125I HIS* 4.3 2.6 + + - -
257I PHE* 3.7 36.9 - + + -
260I TRP* 3.5 37.9 + - + -
261I ASP* 2.8 39.1 + - - -
264I PHE* 3.6 51.4 - + - +
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Residues in contact with ARG 120 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116I TRP* 3.1 40.2 + - - +
117I VAL* 3.1 9.1 + - - +
119I TYR* 1.3 95.1 - - - +
121I GLN* 1.3 58.0 + - - +
123I ARG 3.3 0.5 + - - -
124I GLY 2.9 23.4 + - - -
125I HIS* 2.9 25.9 + - - +
126I LYS 4.1 14.5 + - - -
127I CYS* 3.8 29.0 - - - +
128I GLY 5.4 0.4 - - - +
131I LEU* 3.8 19.9 - - + +
260I TRP* 3.6 33.5 - - - -
264I PHE* 3.7 26.1 - - - -
306I ALA* 5.8 2.2 + - - +
309I MET* 5.8 2.8 - - - +
310I GLU* 4.5 15.0 + - - +
602I 1CA 5.1 3.6 + - - -
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Residues in contact with GLN 121 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117I VAL* 3.0 28.8 + - + +
118I ALA* 3.5 6.9 - - - +
120I ARG* 1.3 74.3 - - - +
122I HIS* 1.3 74.2 + - + +
124I GLY* 3.8 9.1 + - - +
125I HIS 4.9 2.5 - - - -
242I ARG* 2.9 40.3 + - - +
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Residues in contact with HIS 122 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118I ALA* 2.8 35.2 + - + +
119I TYR 4.0 2.0 - - - +
121I GLN* 1.3 88.5 - - + +
123I ARG* 1.3 65.6 + - - +
124I GLY 3.5 0.2 - - - -
242I ARG* 5.6 1.3 - - - -
246I ARG* 5.4 11.0 + - - -
253I TRP* 5.9 1.1 - + - -
257I PHE* 3.6 31.4 - + + -
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Residues in contact with ARG 123 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119I TYR* 3.1 47.6 + - + +
122I HIS* 1.3 86.6 - - - +
124I GLY* 1.3 63.9 + - - +
125I HIS* 3.5 29.3 - - + +
257I PHE* 5.1 9.6 - - - +
261I ASP* 3.3 29.6 + - - -
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Residues in contact with GLY 124 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120I ARG 2.9 8.3 + - - -
121I GLN* 3.8 8.4 + - - -
122I HIS 3.5 2.6 - - - -
123I ARG* 1.3 80.4 - - - +
125I HIS* 1.3 62.7 + - - -
302I GLU* 5.1 4.3 - - - +
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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