Contacts of the helix formed by residues 145 - 151 (chain B) in PDB entry 1XIL
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 PRO 145 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65B LYS* 4.3 10.5 - - + +
69B GLY* 3.8 19.1 - - - -
72B ILE* 4.1 25.4 - - + -
73B ASN* 3.4 20.0 - - - +
143B GLN 3.0 7.2 - - - +
144B ASP* 1.3 85.3 - - + +
146B LEU* 1.3 61.9 + - - +
147B GLN 4.8 2.0 - - - +
148B GLY* 4.5 11.9 - - - +
149B THR* 2.7 43.6 + - + -
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Residues in contact with LEU 146 (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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72B ILE* 5.8 0.8 - - - +
73B ASN* 4.4 3.4 + - - -
125B TRP* 3.9 40.3 - - + +
127B GLY* 4.1 6.1 - - - -
138B ALA* 4.1 17.9 - - + -
140B CYS* 3.7 24.7 - - - -
144B ASP 3.9 1.2 + - - -
145B PRO* 1.3 73.4 - - - +
147B GLN* 1.3 64.0 + - - +
150B THR* 2.7 46.6 + - + +
152B LEU* 3.7 19.3 - - + +
153B ILE 3.9 2.2 - - - +
154B PRO* 3.5 39.7 - - + +
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Residues in contact with GLN 147 (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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145B PRO* 3.5 1.2 - - - +
146B LEU* 1.3 80.2 - - - +
148B GLY* 1.3 62.5 + - - +
151B GLY* 2.9 30.5 + - - +
152B LEU 3.1 18.1 + - - +
153B ILE* 3.5 30.0 - - + +
154B PRO* 4.1 16.0 - - + +
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Residues in contact with GLY 148 (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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145B PRO* 3.7 14.3 + - - +
146B LEU 3.4 0.4 - - - -
147B GLN* 1.3 81.4 - - - +
149B THR* 1.3 62.8 + - - +
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Residues in contact with THR 149 (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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65B LYS* 4.4 12.3 - - + +
140B CYS* 4.5 3.6 - - - -
144B ASP* 3.9 28.8 - - + +
145B PRO* 2.7 33.4 + - + +
146B LEU* 4.3 0.2 - - - -
148B GLY* 1.3 82.2 - - - +
150B THR* 1.3 69.4 + - - +
151B GLY 3.9 0.2 - - - -
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Residues in contact with THR 150 (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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138B ALA* 5.2 4.9 - - + -
139B ALA 5.8 1.3 - - - +
140B CYS* 4.6 6.7 - - - -
146B LEU* 2.7 44.2 + - + +
149B THR* 1.3 87.5 - - - +
151B GLY* 1.3 59.5 + - - +
152B LEU* 3.4 25.7 + - + +
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Residues in contact with GLY 151 (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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128B PHE 4.7 0.3 - - - +
130B LYS* 5.4 4.5 + - - +
147B GLN* 2.9 22.9 + - - +
149B THR 3.9 0.4 - - - -
150B THR* 1.3 77.6 + - - +
152B LEU* 1.3 61.8 + - - +
153B ILE* 3.7 13.2 + - - +
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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