Contacts of the helix formed by residues 119 - 128 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92B ALA* 2.7 36.3 + - + +
93B GLY 4.4 0.4 - - - +
94B VAL 3.5 8.5 + - - -
95B ASP* 3.6 13.2 - - - +
100B GLY* 3.4 22.0 - - - +
103B LEU* 3.9 6.3 - - - +
116B VAL 4.3 5.7 + - - +
117B GLY 3.2 2.9 - - - +
118B GLU* 1.3 79.4 - - - +
120B ALA* 1.3 62.1 + - - +
121B GLU* 3.3 12.1 + - - +
122B PHE* 3.1 36.3 + - + +
123B GLU* 3.4 10.0 + - - +
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Residues in contact with ALA 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B ASP* 3.3 11.6 + - - +
118B GLU 4.2 0.2 - - - -
119B ASN* 1.3 73.2 - - - +
121B GLU* 1.3 58.1 + - - +
123B GLU* 3.4 10.9 + - - +
124B ARG* 3.1 24.1 + - - +
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Residues in contact with GLU 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B ASP* 3.2 21.5 + - - +
100B GLY 5.5 1.1 - - - +
103B LEU* 4.9 3.1 - - + -
104B ARG* 4.3 25.3 - - + +
106B LYS* 5.6 0.3 - - - +
119B ASN* 3.2 5.7 + - - +
120B ALA* 1.3 76.2 - - - +
122B PHE* 1.3 60.6 + - - +
124B ARG* 3.3 33.0 + - - +
125B GLN* 2.7 53.5 + - - +
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Residues in contact with PHE 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B ALA* 4.1 12.1 - - + -
103B LEU* 4.1 17.0 - - + +
111B MET* 3.6 20.4 - - + -
116B VAL* 3.5 42.6 - - + -
119B ASN* 3.1 29.0 + - + +
121B GLU* 1.3 73.4 - - - +
123B GLU* 1.3 71.0 + - + +
125B GLN* 4.1 1.7 - - - +
126B TYR* 3.1 26.9 + + + +
131B LEU* 3.2 31.1 - - + +
133B VAL* 3.2 36.6 - - + -
420B VAL 5.2 3.1 - - - -
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Residues in contact with GLU 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B ASN 3.4 5.7 + - - +
120B ALA* 3.4 15.4 + - - +
121B GLU 3.3 0.4 - - - -
122B PHE* 1.3 84.8 - - + +
124B ARG* 1.3 63.3 + - - +
126B TYR* 3.4 4.3 + - + +
127B LEU* 3.1 49.5 + - + +
418B LYS 4.9 4.6 - - - +
420B VAL* 3.9 29.4 + - + +
421B LYS* 5.8 1.7 - - - +
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Residues in contact with ARG 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B LYS* 5.5 4.4 - - - +
120B ALA 3.1 10.4 + - - +
121B GLU* 3.3 36.3 + - - +
123B GLU* 1.3 81.8 - - - +
125B GLN* 1.3 78.7 + - - +
127B LEU* 4.5 1.9 - - - +
128B SER* 3.1 53.1 + - - -
130B GLU* 4.4 5.9 - - - +
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Residues in contact with GLN 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B LEU* 2.8 39.9 + - - +
104B ARG* 4.4 0.4 - - - +
106B LYS* 4.2 19.5 - - + +
108B ILE 4.9 3.3 - - - +
121B GLU* 2.7 42.5 + - - +
122B PHE 3.5 2.7 + - - +
123B GLU 3.3 0.2 - - - -
124B ARG* 1.3 91.1 - - - +
126B TYR* 1.3 62.2 - - - +
128B SER* 3.8 4.9 - - - -
129B GLY 3.3 1.6 + - - -
130B GLU* 2.9 23.0 + - + +
131B LEU* 2.8 49.7 + - + +
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Residues in contact with TYR 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B PHE* 3.1 24.7 + + + +
123B GLU* 3.8 4.5 - - + +
125B GLN* 1.3 76.7 - - - +
127B LEU* 1.3 78.8 + - + +
129B GLY* 3.2 12.5 + - - -
131B LEU* 3.8 15.0 - - + +
133B VAL* 3.4 37.0 - - + -
171B PRO* 2.4 39.4 + - - +
172B ILE 3.5 20.6 - - - -
173B LYS* 5.1 0.2 - - - -
174B TYR* 3.5 34.3 + + - +
420B VAL* 4.9 17.5 - - + -
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Residues in contact with LEU 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B GLU* 3.1 43.7 + - + +
124B ARG* 4.7 2.2 - - - +
126B TYR* 1.3 95.8 - - + +
128B SER* 1.3 62.0 + - - +
129B GLY 3.6 0.3 + - - -
174B TYR* 4.3 25.6 - - + +
175B ASN 5.1 1.2 - - - +
178B GLY* 6.0 1.6 - - - -
420B VAL* 5.6 6.7 - - + -
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Residues in contact with SER 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B ARG* 3.1 48.3 + - - -
125B GLN* 3.6 5.0 + - - -
127B LEU* 1.3 76.5 - - - +
129B GLY* 1.3 59.9 + - - +
130B GLU* 3.8 6.6 - - - +
175B ASN 4.3 8.8 - - - +
176B LYS* 4.4 10.7 - - - +
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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