Contacts of the strand formed by residues 179 - 184 (chain A) in PDB entry 1L3C
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 179 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A THR* 5.5 3.6 - - + -
18A ALA* 5.9 3.1 - - + +
21A VAL* 4.1 40.2 - - + -
133A THR* 4.3 12.8 - - + -
134A ALA 3.8 8.5 - - - +
135A ILE* 3.9 18.4 - - + -
157A THR 3.9 0.5 - - - +
158A GLU* 3.5 3.7 - - - -
159A LEU* 2.8 36.4 + - - +
161A ILE* 6.0 2.2 - - + -
177A ASN* 3.5 11.0 - - + +
178A PRO* 1.3 79.5 - - - +
180A ALA* 1.3 72.2 + - - +
181A LEU* 4.3 3.5 + - + +
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Residues in contact with ALA 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A VAL 3.5 0.9 - - - +
134A ALA* 2.9 33.3 + - - +
140A LYS* 3.8 36.5 - - + +
156A ILE* 4.2 11.2 - - + -
157A THR 3.3 5.6 - - - +
158A GLU* 3.8 17.2 + - + +
179A VAL* 1.3 73.8 - - - +
181A LEU* 1.3 68.0 + - - +
182A ILE* 4.1 3.4 - - + -
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Residues in contact with LEU 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A VAL* 4.0 25.4 - - + +
24A LEU* 3.7 40.8 - - + -
25A ILE* 4.0 19.5 - - + -
28A LEU* 4.2 18.6 - - + -
131A ILE* 4.5 7.0 - - + -
132A VAL 3.4 4.7 - - - +
133A THR* 4.0 18.8 - - - +
156A ILE* 3.2 4.2 - - - -
157A THR* 2.8 39.6 + - - +
159A LEU* 5.5 3.1 - - + -
179A VAL* 4.5 4.9 - - + +
180A ALA* 1.3 82.7 - - - +
182A ILE* 1.3 61.5 + - - +
183A TYR* 3.8 5.1 - - + -
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Residues in contact with ILE 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A ILE 3.9 0.3 - - - +
131A ILE* 3.5 1.7 - - - -
132A VAL* 2.8 41.2 + - + +
134A ALA* 3.8 28.5 - - + -
140A LYS* 4.0 13.2 - - - -
143A ALA* 4.1 22.2 - - + -
144A MSE 4.1 12.8 - - + +
147A LEU* 3.8 16.4 - - + +
154A VAL* 3.5 29.6 - - + -
155A ASN 3.3 4.7 - - - +
156A ILE* 3.9 22.9 - - + -
180A ALA* 4.2 3.8 - - + +
181A LEU* 1.3 76.6 - - - +
183A TYR* 1.3 59.7 + - - +
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Residues in contact with TYR 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A LEU* 3.6 42.0 - - + +
130A ILE 3.3 12.1 - - - +
131A ILE* 4.2 13.9 - - + -
147A LEU* 5.2 0.7 - - - -
154A VAL* 3.6 3.4 - - - -
155A ASN* 2.9 73.1 + - + +
156A ILE 5.3 0.3 + - - -
157A THR* 3.7 25.1 + - - -
181A LEU* 3.8 13.7 - - + -
182A ILE* 1.3 76.1 - - - +
184A THR* 1.3 74.1 + - - +
185A GLY* 5.7 0.7 - - - -
20D GLU* 5.5 0.7 + - - -
163D ARG* 5.9 2.1 - - - -
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Residues in contact with THR 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A GLY 4.5 1.6 + - - -
129A ARG* 4.1 5.7 - - - +
130A ILE* 3.2 36.4 + - + +
147A LEU* 4.0 24.2 - - + -
152A PHE* 3.5 47.8 - - + -
153A ASP 3.4 5.6 - - - +
154A VAL* 5.1 0.4 - - + -
155A ASN* 4.6 0.2 - - - -
183A TYR* 1.3 88.2 - - - +
185A GLY* 1.3 70.3 + - - +
186A VAL* 3.8 4.7 + - - +
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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