Contacts of the helix formed by residues 127 - 139 (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 THR 127 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A CYS* 3.5 29.8 - - + -
126A PHE* 3.7 17.9 - - + -
169A TRP* 3.5 31.5 - - + +
123B CYS 4.0 0.2 + - - -
124B LYS 2.8 21.5 + - - +
126B PHE* 1.3 79.1 - - - +
128B PRO* 1.3 70.8 - - - +
130B LEU* 3.3 21.0 + - - +
131B LEU* 3.0 21.3 + - - +
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Residues in contact with PRO 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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126A PHE* 3.4 24.2 - - + -
169A TRP 3.2 17.3 - - - +
170A TYR 3.7 17.9 - - - +
171A ASP* 3.9 14.4 - - + +
172A HIS* 5.2 2.9 - - + +
173A TYR* 4.0 22.4 - - + -
126B PHE 3.5 2.7 - - - +
127B THR* 1.3 83.7 - - - +
129B GLY* 1.3 59.4 + - - +
131B LEU* 3.7 10.9 - - + +
132B LYS* 3.1 32.4 + - - +
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Residues in contact with GLY 129 (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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168A PHE* 3.3 43.8 - - - -
169A TRP 3.0 11.6 + - - -
171A ASP* 4.0 9.8 - - - +
128B PRO* 1.3 78.9 - - - +
130B LEU* 1.3 60.8 + - - +
132B LYS* 3.5 4.7 + - - +
133B ALA* 3.1 16.6 + - - +
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Residues in contact with LEU 130 (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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168A PHE* 4.1 9.2 - - + -
169A TRP* 3.9 22.2 - - + +
52B LEU* 3.8 28.3 - - + -
53B TYR* 4.0 8.7 - - - +
80B VAL* 4.8 6.3 - - + -
124B LYS* 3.4 44.2 - - + +
125B LEU* 4.5 13.7 - - + +
127B THR* 3.3 14.3 + - - +
129B GLY* 1.3 74.1 - - - +
131B LEU* 1.3 61.4 + - - +
133B ALA* 3.3 2.9 + - + -
134B TYR* 2.8 52.5 + - + -
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Residues in contact with LEU 131 (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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125B LEU 3.4 18.8 + - - +
126B PHE* 3.4 25.1 - - + +
127B THR 3.0 16.6 + - - +
128B PRO* 3.7 8.5 - - + +
130B LEU* 1.3 76.9 - - - +
132B LYS* 1.3 58.7 + - + +
134B TYR* 3.8 3.8 - - - +
135B ARG* 2.9 43.0 + - - +
146B LEU* 4.5 13.9 - - + -
147B PRO* 3.8 27.4 - - + -
148B PHE* 4.0 10.8 - - + -
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Residues in contact with LYS 132 (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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171A ASP* 2.7 37.4 + - - +
172A HIS* 4.4 10.3 - - - +
128B PRO* 3.1 21.8 + - - +
129B GLY* 3.8 4.3 - - - +
131B LEU* 1.3 78.2 - - + +
133B ALA* 1.3 62.0 + - - +
135B ARG* 3.4 5.6 + - - +
136B THR* 3.0 30.2 + - - +
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Residues in contact with ALA 133 (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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168A PHE* 4.0 20.2 - - + -
49B LEU* 4.3 15.0 - - + -
52B LEU* 4.3 8.7 - - + -
129B GLY 3.1 15.2 + - - +
130B LEU* 3.7 7.2 - - + +
132B LYS* 1.3 79.8 - - - +
134B TYR* 1.3 58.1 + - + +
136B THR* 3.4 4.9 + - - -
137B ILE* 2.9 38.5 + - + +
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Residues in contact with TYR 134 (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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49B LEU* 3.6 32.9 - - + +
80B VAL* 4.3 8.4 - - + +
82B PRO* 3.7 18.5 - - - +
96B PHE* 3.4 36.3 - + + -
98B GLU* 3.8 6.3 + - - -
125B LEU* 3.2 35.9 - - + +
130B LEU* 2.8 42.8 + - + +
131B LEU* 3.8 0.4 - - - +
133B ALA* 1.3 73.9 - - + +
135B ARG* 1.3 58.3 + - - +
137B ILE* 4.9 0.4 - - - -
138B GLY* 2.8 30.9 + - - +
140B ILE 5.2 0.2 + - - -
147B PRO* 3.6 34.1 - - + +
148B PHE* 3.9 15.3 - + + -
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Residues in contact with ARG 135 (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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131B LEU* 2.9 26.7 + - - +
132B LYS* 4.0 4.7 - - - +
134B TYR* 1.3 76.4 - - - +
136B THR* 1.3 57.6 + - - +
139B GLY* 3.0 27.7 + - - -
140B ILE* 2.9 49.0 + - - +
141B ASN* 3.6 29.5 + - - +
142B ASP 3.0 24.0 + - - -
143B GLU* 4.2 10.3 + - - +
145B ILE 2.9 24.3 + - - -
146B LEU* 4.1 14.5 - - - +
147B PRO* 3.8 20.9 - - + +
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Residues in contact with THR 136 (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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132B LYS* 3.0 20.8 + - - +
133B ALA* 3.7 6.1 - - - -
135B ARG* 1.3 79.5 - - - +
137B ILE* 1.3 70.4 + - + +
139B GLY* 3.9 4.9 + - - -
141B ASN* 5.6 0.4 - - - +
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Residues in contact with ILE 137 (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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48B HIS* 3.6 45.5 - - + +
49B LEU* 3.4 29.8 - - + -
52B LEU* 4.8 8.5 - - + -
92B HIS 5.0 2.6 - - - +
94B ILE* 4.8 6.7 - - + +
96B PHE* 3.9 13.0 - - + -
133B ALA* 2.9 17.0 + - + +
134B TYR* 4.2 1.3 - - - +
136B THR* 1.3 85.9 - - + +
138B GLY* 1.3 61.8 + - - +
139B GLY* 3.5 0.5 + - - -
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Residues in contact with GLY 138 (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 HIS 4.9 0.9 - - - -
93B LYS* 3.1 12.7 - - - +
94B ILE* 2.9 46.8 + - - +
96B PHE* 4.0 8.6 - - - -
134B TYR 2.8 19.4 + - - -
137B ILE* 1.3 75.0 - - - +
139B GLY* 1.3 60.1 + - - +
140B ILE* 3.4 4.1 + - - +
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Residues in contact with GLY 139 (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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93B LYS* 3.6 26.9 + - - -
135B ARG 3.0 14.5 + - - -
136B THR 3.9 3.8 + - - -
137B ILE 3.3 3.4 - - - -
138B GLY* 1.3 77.7 - - - +
140B ILE* 1.3 61.5 + - - +
141B ASN* 3.6 12.7 + - - -
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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