Contacts of the helix formed by residues 117 - 126 (chain B) in PDB entry 1D02
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 117 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121A ARG* 3.2 31.1 + - - +
115B ARG 4.5 2.2 - - - +
116B GLY* 1.3 74.2 - - - +
118B ALA* 1.3 66.5 + - - +
119B HIS* 3.1 11.0 - - + -
120B GLU* 3.0 39.1 + - - +
162B ARG* 5.6 2.2 - - - +
6C T 3.5 1.4 + - - -
3D C 3.4 23.1 + - + +
4D A 2.8 38.5 + - - -
5D A 2.9 12.8 + - - -
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Residues in contact with ALA 118 (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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121A ARG* 4.5 5.2 - - - +
100B LYS* 5.0 1.9 - - - +
102B GLN* 3.7 9.1 - - - +
117B ASN* 1.3 78.6 - - - +
119B HIS* 1.3 62.9 + - - +
120B GLU 2.9 0.4 - - - -
121B ARG* 2.9 31.2 + - - +
5C A 3.5 41.5 - - + +
6C T 3.1 22.6 + - + +
5D A 4.4 6.3 - - - +
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Residues in contact with HIS 119 (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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100B LYS* 4.3 17.0 - - + -
102B GLN* 3.0 29.2 + - + +
116B GLY 3.5 20.4 - - - -
117B ASN* 3.5 12.4 - - + -
118B ALA* 1.3 76.5 - - - +
120B GLU* 1.3 60.9 + - + +
121B ARG 3.0 1.3 + - - -
122B SER* 2.7 30.7 + - - -
152B PHE* 4.3 11.6 - + + -
156B ILE* 3.8 21.1 - - + -
162B ARG* 3.5 17.2 - - - -
165B GLU* 2.8 29.8 + - - -
166B ILE* 4.1 9.2 - - + -
169B TRP* 3.5 25.7 - + - -
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Residues in contact with GLU 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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120A GLU 3.9 5.2 - - - +
121A ARG* 2.9 50.5 + - - +
124A LYS* 2.7 38.2 + - + +
117B ASN* 3.0 30.9 + - + +
118B ALA 2.9 1.0 + - - -
119B HIS* 1.3 83.8 - - + +
121B ARG* 1.3 57.4 + - - +
123B CYS* 2.9 27.9 + - - +
165B GLU* 4.4 4.9 - - - +
169B TRP* 3.6 29.4 - - + -
3D C 4.1 5.9 + - - -
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Residues in contact with ARG 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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117A ASN* 3.2 29.0 - - - +
118A ALA* 4.6 1.1 - - - +
120A GLU* 3.0 45.0 + - + +
121A ARG* 3.9 18.6 - - + +
100B LYS* 4.0 12.4 - - - +
118B ALA* 2.9 17.1 + - - +
120B GLU* 1.3 78.4 - - - +
122B SER* 1.3 61.2 + - - +
123B CYS 3.0 1.4 + - - -
124B LYS* 3.1 29.2 + - - +
3C C 3.6 6.5 + - - +
4C A 3.0 35.4 + - - +
5C A 3.0 49.4 + - - +
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Residues in contact with SER 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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98B GLU* 5.2 5.2 - - - -
100B LYS* 3.8 31.4 - - - +
119B HIS 2.7 21.3 + - - -
120B GLU 3.1 0.2 - - - -
121B ARG* 1.3 76.9 - - - +
123B CYS* 1.3 63.6 + - - +
124B LYS* 3.0 8.8 + - - -
125B LEU* 3.2 25.9 + - - +
126B PHE* 4.8 2.5 - - - -
150B VAL* 4.3 19.5 - - - +
152B PHE* 4.3 12.3 - - - -
169B TRP* 4.7 1.6 - - - -
170B TYR* 4.9 3.0 + - - -
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Residues in contact with CYS 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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123A CYS* 3.5 26.0 - - - +
124A LYS* 3.5 13.2 - - - +
127A THR* 3.5 24.5 - - - -
120B GLU 2.9 16.0 + - - +
122B SER* 1.3 75.6 - - - +
124B LYS* 1.3 60.4 + - - +
125B LEU 2.9 6.3 - - - -
126B PHE* 2.9 34.5 + - + +
127B THR 4.0 0.5 + - - -
169B TRP* 3.5 32.3 - - - -
170B TYR* 5.8 0.2 - - - -
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Residues in contact with LYS 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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120A GLU* 2.7 42.7 + - + +
123A CYS* 3.5 25.3 - - + +
165A GLU* 4.4 7.3 + - - -
169A TRP* 4.1 11.4 - - + +
53B TYR* 4.8 0.2 + - - -
80B VAL* 3.7 22.5 - - - +
98B GLU* 6.5 0.7 - - - -
121B ARG* 3.1 16.7 + - - +
122B SER* 3.0 6.0 + - - +
123B CYS* 1.3 76.7 - - - +
125B LEU* 1.3 70.8 + - + +
126B PHE 3.1 0.4 - - - -
127B THR* 2.8 28.5 + - - -
130B LEU* 3.4 26.3 - - + +
3C C 3.9 12.9 + - - -
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Residues in contact with LEU 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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97B GLY 5.7 0.4 - - - -
98B GLU* 3.5 33.0 - - + +
122B SER* 3.5 15.5 - - - +
123B CYS 2.9 1.2 - - - -
124B LYS* 1.3 90.5 - - + +
126B PHE* 1.3 56.6 + - - +
127B THR 3.3 1.9 + - - +
130B LEU* 4.5 9.3 - - + +
131B LEU* 3.4 28.8 + - - +
134B TYR* 3.2 39.6 - - + +
148B PHE* 3.4 49.3 - - + -
150B VAL* 4.0 4.9 - - + -
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Residues in contact with PHE 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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126A PHE* 3.7 29.6 - - + +
127A THR* 3.8 21.3 - - + +
128A PRO* 3.4 31.4 - - + -
122B SER 4.8 0.7 - - - -
123B CYS* 2.9 32.2 + - - +
125B LEU* 1.3 76.9 - - - +
127B THR* 1.3 65.8 + - - +
128B PRO* 3.5 2.4 - - - +
131B LEU* 3.4 18.5 - - + +
146B LEU* 3.4 28.5 - - + -
148B PHE* 3.8 9.6 - + - -
170B TYR* 3.5 51.6 - + - -
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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