Contacts of the helix formed by residues 172 - 181 (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 VAL 172 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165B YOF 4.9 0.2 - - - -
169B YOF 2.9 24.4 + - - +
170B LYS* 3.2 1.7 - - + -
171B ASN* 1.3 95.0 - - - +
173B ARG* 1.3 63.0 + - - +
174B PRO* 3.2 11.2 - - + -
175B ASP* 2.9 52.1 + - + +
176B YOF 3.5 3.6 + - - -
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Residues in contact with ARG 173 (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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161A TRP* 5.3 4.6 - - - -
115B SER 3.5 10.8 + - - -
116B VAL* 3.0 39.9 + - + +
118B VAL* 2.8 24.2 + - - +
120B GLY 3.1 25.7 + - - +
160B VAL* 3.1 27.6 + - + +
162B GLU* 5.1 5.3 + - - +
165B YOF 3.1 48.2 + - + +
171B ASN 2.9 10.0 + - - +
172B VAL* 1.3 71.2 - - - +
174B PRO* 1.3 68.9 - - + +
175B ASP 3.1 0.5 + - - -
176B YOF 3.2 9.4 + - + +
177B LEU* 3.0 21.6 + - + +
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Residues in contact with PRO 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B THR* 5.9 1.6 - - + -
116B VAL* 4.4 20.8 - - + -
171B ASN 5.0 0.4 - - - +
172B VAL* 3.3 13.7 - - + -
173B ARG* 1.3 93.8 - - + +
175B ASP* 1.3 60.6 + - - +
177B LEU* 3.4 3.6 + - + +
178B LYS* 2.9 28.6 + - - +
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Residues in contact with ASP 175 (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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169B YOF 3.8 25.5 - - + -
172B VAL* 2.9 35.5 + - + +
174B PRO* 1.3 77.2 - - - +
176B YOF 1.3 65.8 + - - +
178B LYS* 3.4 8.8 + - - +
179B ALA* 3.1 22.9 + - - +
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Residues in contact with YOF 176 (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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17B HIS 5.4 0.2 - - - -
18B ILE* 3.2 37.5 - - + -
77B PHE* 3.7 20.3 - - - -
158B ILE* 4.3 1.6 - - + -
159B ASP 2.7 30.8 + - - -
160B VAL* 4.3 1.8 - - + -
164B ALA* 3.7 22.6 - - + +
165B YOF 3.5 44.2 - + + -
169B YOF 3.7 27.4 - + + -
172B VAL 3.5 1.8 + - - -
173B ARG* 3.2 9.1 + - + +
175B ASP* 1.3 76.5 + - - +
177B LEU* 1.3 83.8 + - + +
179B ALA* 3.1 2.6 + - + +
180B ILE* 3.0 38.1 + - + +
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Residues in contact with LEU 177 (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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111B LEU 5.1 0.2 - - - -
112B THR* 3.9 44.2 - - + +
115B SER* 4.1 9.4 - - - +
116B VAL* 4.1 10.1 - - + -
158B ILE* 3.9 36.6 - - + -
160B VAL* 4.0 13.9 - - + -
173B ARG* 3.0 17.1 + - + +
174B PRO* 3.8 6.5 - - + +
175B ASP 3.3 0.2 - - - -
176B YOF 1.3 91.9 + - + +
178B LYS* 1.3 61.4 + - - +
179B ALA 3.3 0.3 + - - -
180B ILE* 3.4 14.3 - - + +
181B TRP* 2.8 34.3 + - + +
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Residues in contact with LYS 178 (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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174B PRO 2.9 18.1 + - - +
175B ASP* 3.8 9.2 - - - +
176B YOF 3.3 0.4 - - - -
177B LEU* 1.3 79.8 - - - +
179B ALA* 1.3 61.1 + - - +
181B TRP* 3.7 19.2 + - + +
182B ASN* 3.9 8.3 + - - +
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Residues in contact with ALA 179 (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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17B HIS* 3.7 23.6 - - + +
169B YOF 3.1 30.5 - - + +
175B ASP 3.1 14.5 + - - +
176B YOF 3.1 4.9 + - + +
178B LYS* 1.3 76.0 - - - +
180B ILE* 1.3 66.2 + - - +
182B ASN* 2.9 31.3 + - - +
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Residues in contact with ILE 180 (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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17B HIS* 5.2 1.1 - - - -
18B ILE* 4.1 15.7 - - + -
77B PHE* 3.9 24.0 - - + -
81B LEU* 4.1 15.0 - - + -
158B ILE* 4.3 27.1 - - + -
176B YOF 3.0 48.1 + - + +
177B LEU* 3.4 25.1 - - + +
179B ALA* 1.3 77.9 - - - +
181B TRP* 1.3 70.1 + - + +
183B VAL* 3.0 19.7 + - + +
184B ILE* 3.5 11.1 - - + +
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Residues in contact with TRP 181 (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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86B GLY* 3.4 16.1 - - - -
87B GLY 4.1 4.9 + - - +
104B PHE* 4.7 1.8 - + + -
107B PHE* 3.8 24.5 - + - -
108B LYS* 3.5 60.3 - - + +
111B LEU* 3.9 23.8 - - + -
112B THR* 3.5 26.5 + - - -
156B LEU* 4.4 7.9 - - + -
158B ILE* 5.5 3.4 - - + -
177B LEU* 2.8 37.7 + - + +
178B LYS* 3.7 14.4 - - + +
179B ALA 3.1 1.0 + - - -
180B ILE* 1.3 79.5 - - + +
182B ASN* 1.3 62.8 + - - +
183B VAL 3.3 1.0 + - - -
184B ILE* 3.7 20.4 + - + +
186B TRP* 4.2 16.1 + + - -
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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