Contacts of the strand formed by residues 168 - 173 (chain C) in PDB entry 1L9W
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 ILE 168 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4C VAL* 4.2 19.5 - - + -
11C ILE* 4.2 32.5 - - + -
112C MET* 5.0 5.6 - - - -
137C TYR* 5.8 1.6 - - + -
138C VAL 3.2 4.0 + - - +
139C VAL* 3.4 24.9 - - + +
140C MET 3.0 22.2 + - - +
166C ALA* 4.3 0.9 - - - -
167C ASP* 1.3 84.1 - - + +
169C PRO* 1.3 70.2 - - - +
199C PRO* 3.5 24.2 - - + +
201C ILE* 3.6 37.2 - - + -
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Residues in contact with PRO 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140C MET 3.6 5.2 - - - +
158C LEU* 3.9 26.7 - - + +
161C MET* 3.8 27.6 - - + -
162C GLN* 4.3 10.1 - - + +
166C ALA* 4.2 4.7 - - + -
167C ASP 4.0 0.9 - - - -
168C ILE* 1.3 88.6 - - - +
170C LYS* 1.3 57.6 + - - +
191C MET* 5.3 0.2 - - + -
198C ARG* 3.9 19.7 - - + -
199C PRO 3.1 17.3 - - - +
200C VAL* 3.5 17.1 - - + +
201C ILE 3.1 22.9 + - - +
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Residues in contact with LYS 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C GLU* 4.6 1.2 + - - -
82C ARG* 4.0 5.3 - - - +
114C ASP* 4.5 2.0 + - - +
139C VAL* 4.0 20.6 - - + +
140C MET 2.7 15.8 + - - +
141C SER* 3.2 17.4 - - - -
142C ASN 3.0 22.5 + - - -
143C HIS* 4.6 5.4 - - - +
158C LEU* 4.3 1.7 - - - +
161C MET* 3.4 9.7 - - - +
168C ILE 4.3 0.2 - - - +
169C PRO* 1.3 75.8 - - - +
171C ILE* 1.3 63.8 + - - +
172C ALA* 5.1 1.8 - - - -
201C ILE* 3.3 28.0 - - + +
203C MET* 3.9 15.0 - - - -
225C PHE* 3.3 22.4 - - + -
303C DHS 3.0 46.7 + - - +
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Residues in contact with ILE 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142C ASN* 3.4 33.0 - - + +
143C HIS* 5.3 0.2 - - - -
154C MET* 3.9 35.2 - - + +
157C ARG* 4.5 15.0 - - + +
158C LEU* 4.1 18.8 - - + +
161C MET* 5.0 0.7 - - + -
170C LYS* 1.3 76.8 - - - +
172C ALA* 1.3 64.1 + - - +
173C VAL* 3.8 17.0 - - + -
184C LEU* 4.4 11.9 - - + -
201C ILE 3.2 4.8 + - - -
202C THR* 3.4 25.7 - - + -
203C MET* 3.1 25.7 + - - +
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Residues in contact with ALA 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142C ASN 3.1 6.3 + - - -
143C HIS* 3.3 26.5 - - + +
144C ASP 3.1 22.3 + - - -
170C LYS* 5.1 0.9 - - - -
171C ILE* 1.3 74.7 - - - +
173C VAL* 1.3 62.5 + - - +
203C MET* 3.3 29.2 - - + -
205C MET* 3.8 10.4 - - + +
303C DHS 4.2 12.6 - - + +
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Residues in contact with VAL 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C ASP* 3.5 12.1 - - + +
147C GLN 4.0 3.4 - - - +
148C THR* 3.7 26.2 - - + +
149C PRO* 3.7 23.8 - - + -
154C MET* 3.9 6.1 - - - -
171C ILE* 3.8 21.5 - - + -
172C ALA* 1.3 79.9 - - - +
174C MET* 1.3 54.9 + - - +
175C PRO* 3.6 0.2 - - - +
184C LEU* 3.8 29.6 - - + -
203C MET 3.0 10.3 + - - +
204C SER* 3.4 7.4 - - - +
205C MET* 2.8 35.5 + - - +
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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