Contacts of the helix formed by residues 119 - 128 (chain D) in PDB entry 3DLX
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 ASN 119 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92D ALA* 2.7 33.0 + - + +
93D GLY 4.3 2.2 - - - +
94D VAL* 3.3 13.4 + - - -
95D ASP* 3.5 21.6 - - - +
100D GLY* 3.8 3.6 - - - -
103D LEU* 3.7 18.4 - - - +
116D VAL 4.4 7.1 - - - +
117D GLY 3.5 1.2 - - - +
118D GLU* 1.3 80.1 - - - +
120D ALA* 1.3 63.5 + - - +
121D GLU* 3.2 8.1 + - - +
122D PHE* 3.0 24.8 + - + +
123D GLU* 3.3 18.9 + - - +
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Residues in contact with ALA 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D ASP* 4.6 8.9 - - + +
118D GLU 4.2 0.4 - - - -
119D ASN* 1.3 71.0 + - - +
121D GLU* 1.3 60.3 + - - +
123D GLU* 3.1 10.4 + - - +
124D ARG* 2.8 28.6 + - - +
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Residues in contact with GLU 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D ASP* 4.8 12.8 - - + +
100D GLY 5.7 1.3 - - - +
103D LEU* 5.1 2.7 - - + -
104D ARG* 4.2 25.6 - - + +
106D LYS* 5.0 2.4 - - - +
119D ASN* 3.2 8.3 + - - +
120D ALA* 1.3 76.7 - - - +
122D PHE* 1.3 57.7 + - - +
124D ARG* 3.2 39.2 + - - +
125D GLN* 2.8 59.1 + - - +
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Residues in contact with PHE 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92D ALA* 4.0 8.1 - - + -
103D LEU* 3.8 19.3 - - + +
111D MET* 3.9 16.4 - - + -
116D VAL* 3.3 48.2 - - + -
119D ASN* 3.0 32.6 + - + +
121D GLU* 1.3 77.7 - - - +
123D GLU* 1.3 60.3 + - + +
125D GLN* 3.3 5.3 + - - +
126D TYR* 2.9 41.1 + + + +
131D LEU* 3.2 30.5 - - + -
133D VAL* 3.6 31.2 - - + -
420D VAL 5.1 0.4 - - - -
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Residues in contact with GLU 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D VAL 5.8 1.1 - - - +
119D ASN 3.3 9.2 + - - +
120D ALA* 3.1 13.2 + - - +
122D PHE* 1.3 82.7 - - + +
124D ARG* 1.3 65.3 + - - +
126D TYR* 4.6 3.4 - - - -
127D LEU* 3.0 38.5 + - + +
420D VAL* 6.3 3.6 - - + -
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Residues in contact with ARG 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D ALA 2.8 12.9 + - - +
121D GLU* 3.2 41.1 + - - +
122D PHE 3.2 0.2 - - - -
123D GLU* 1.3 78.0 - - - +
125D GLN* 1.3 56.3 + - - +
126D TYR 3.2 0.2 + - - -
127D LEU* 4.3 1.1 - - - +
128D SER* 2.6 59.0 + - - +
130D GLU* 3.4 33.5 + - - -
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Residues in contact with GLN 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D LEU* 3.1 37.7 + - - +
106D LYS* 3.7 14.5 - - - +
108D ILE 5.1 2.4 - - - +
121D GLU* 2.8 49.9 + - - +
122D PHE 3.8 3.8 - - - +
124D ARG* 1.3 81.3 - - - +
126D TYR* 1.3 58.2 + - - +
128D SER* 3.3 7.7 + - - -
130D GLU* 2.6 57.9 + - + +
131D LEU* 3.1 27.6 + - + +
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Residues in contact with TYR 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122D PHE* 2.9 31.5 + + + +
123D GLU* 4.1 4.3 - - - +
125D GLN* 1.3 73.3 - - - +
127D LEU* 1.3 62.4 + - + +
129D GLY* 3.0 18.7 + - - -
131D LEU* 4.1 13.3 - - + +
133D VAL* 3.8 33.9 - - + -
135D LEU* 4.7 13.1 - - + +
171D PRO* 2.6 38.8 + - - +
172D ILE 3.9 19.3 - - - -
173D LYS* 4.8 0.7 - - - -
174D TYR* 3.5 31.4 + + - +
414D MET* 5.5 3.3 - - - -
420D VAL* 4.1 31.6 - - + -
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Residues in contact with LEU 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D GLU* 3.0 27.3 + - + +
124D ARG* 4.3 0.9 - - - +
126D TYR* 1.3 77.6 - - + +
128D SER* 1.3 57.4 + - - +
129D GLY 3.3 1.2 + - - -
174D TYR* 3.7 29.5 - - + +
178D GLY 3.9 19.2 + - - -
417D GLY* 3.8 26.0 - - - +
418D LYS* 4.1 27.8 - - - +
420D VAL* 4.7 19.7 - - + -
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Residues in contact with SER 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124D ARG* 2.6 48.3 + - - -
125D GLN* 3.3 13.5 + - - -
127D LEU* 1.3 71.7 - - - +
129D GLY* 1.3 59.4 + - - +
130D GLU* 3.6 8.5 + - - +
175D ASN 4.9 4.3 - - - -
176D LYS* 4.5 16.0 - - - +
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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