Contacts of the strand formed by residues 154 - 166 (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 154 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144A MSE 4.1 22.6 - - - +
147A LEU* 3.5 29.8 - - + -
148A ARG* 3.7 27.8 + - + +
152A PHE* 3.6 15.0 + - + +
153A ASP* 1.3 75.2 - - - +
155A ASN* 1.3 74.0 + - - +
182A ILE* 3.5 29.8 - - + -
183A TYR 3.6 5.8 - - - +
184A THR* 5.1 0.4 - - + -
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Residues in contact with ASN 155 (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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144A MSE 4.9 1.1 - - - -
153A ASP* 3.9 10.5 + - - +
154A VAL* 1.3 82.7 - - - +
156A ILE* 1.3 63.2 + - - +
182A ILE* 3.3 7.8 - - - +
183A TYR* 2.9 74.1 + - + +
185A GLY* 4.4 8.5 - - - +
164D GLY 5.7 2.7 - - - +
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Residues in contact with ILE 156 (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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140A LYS* 4.5 5.6 - - + -
144A MSE 4.1 16.6 - - - -
155A ASN* 1.3 78.6 - - - +
157A THR* 1.3 72.7 + - - +
158A GLU* 4.9 1.8 - - + +
180A ALA* 4.2 12.8 - - + -
181A LEU 3.2 10.5 - - - +
182A ILE* 3.9 22.7 - - + -
183A TYR* 4.5 0.6 + - - -
137C LEU* 3.7 26.2 - - + -
163D ARG* 3.3 3.8 - - - +
164D GLY* 2.8 53.4 + - - +
171D THR* 4.1 7.4 - - + -
173D MSE 4.1 17.9 - - + -
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Residues in contact with THR 157 (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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24A LEU* 4.2 11.2 - - + -
156A ILE* 1.3 77.8 + - - +
158A GLU* 1.3 64.5 + - - +
159A LEU* 4.0 13.7 - - + +
179A VAL 3.9 1.0 - - - +
180A ALA* 3.3 1.4 - - - -
181A LEU* 2.8 41.7 + - - +
183A TYR* 3.7 20.8 + - - -
20D GLU* 3.5 28.9 + - + +
161D ILE* 3.7 20.2 - - + -
162D ALA 3.2 5.6 - - - +
163D ARG* 4.1 7.5 - - + +
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Residues in contact with GLU 158 (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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140A LYS* 3.1 38.0 + - - +
156A ILE* 4.9 3.0 - - + +
157A THR* 1.3 72.7 - - - +
159A LEU* 1.3 63.5 + - - +
160A ASN* 4.8 7.7 + - - +
178A PRO* 3.8 20.3 - - - +
179A VAL 3.5 7.7 - - - +
180A ALA* 3.8 15.7 - - + -
137C LEU* 5.3 4.2 - - - +
140C LYS* 5.3 3.3 + - - -
158C GLU* 4.7 9.9 - - - +
160D ASN 3.7 1.2 - - - +
161D ILE* 3.5 5.5 - - - -
162D ALA* 2.7 37.3 + - + +
173D MSE 3.4 26.7 - - + +
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Residues in contact with LEU 159 (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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20A GLU* 4.2 20.6 - - + +
21A VAL* 4.5 17.3 - - + -
24A LEU* 4.0 20.6 - - + -
157A THR* 4.0 9.6 - - + +
158A GLU* 1.3 83.4 - - - +
160A ASN* 1.3 62.1 + - - +
161A ILE* 4.0 19.4 + - + +
177A ASN 4.5 1.0 - - - +
178A PRO* 3.4 6.9 - - - +
179A VAL* 2.8 36.4 + - - +
181A LEU* 5.5 4.0 - - + -
20D GLU* 4.2 9.6 - - + -
159D LEU* 5.6 8.5 - - + -
160D ASN 4.5 0.4 - - - +
161D ILE* 3.6 34.5 - - + -
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Residues in contact with ASN 160 (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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158A GLU* 4.8 9.1 + - - +
159A LEU* 1.3 78.5 + - - +
161A ILE* 1.3 62.0 + - - +
176A ARG 4.7 1.8 - - - +
178A PRO* 3.5 31.3 - - - +
160B ASN* 5.6 10.3 - - + +
162B ALA* 5.7 0.9 - - - +
175B SER* 4.2 7.8 + - - -
160C ASN* 4.1 24.7 + - - +
158D GLU 3.7 1.0 - - - +
159D LEU* 3.7 3.8 - - - +
160D ASN* 2.9 54.1 + - + +
162D ALA* 6.3 0.6 - - - +
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Residues in contact with ILE 161 (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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18A ALA* 4.4 8.3 - - + -
20A GLU* 3.7 45.8 - - + +
21A VAL* 4.1 21.8 - - + -
159A LEU* 4.1 13.4 + - + +
160A ASN* 1.3 81.4 - - - +
162A ALA* 1.3 66.4 + - - +
163A ARG* 4.4 5.4 - - + -
175A SER* 3.5 4.2 + - - -
176A ARG* 3.0 45.8 + - + +
177A ASN 5.8 1.8 + - - +
179A VAL* 6.0 1.6 - - + -
157D THR* 3.8 17.7 - - + -
158D GLU 3.6 2.7 - - - -
159D LEU* 3.7 15.9 - - + -
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Residues in contact with ALA 162 (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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161A ILE* 1.3 76.0 - - - +
163A ARG* 1.3 62.4 + - - +
173A MSE 3.7 19.4 - - + +
174A VAL 3.2 11.0 - - - +
175A SER* 4.4 2.7 - - - +
160B ASN* 5.6 1.1 - - - +
178B PRO* 4.2 24.5 - - + -
157D THR* 3.3 7.1 - - - +
158D GLU* 2.9 39.6 + - + +
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Residues in contact with ARG 163 (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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4A ASP* 2.9 34.8 + - - +
18A ALA* 3.5 14.5 - - - +
19A MSE 3.7 3.6 - - - +
20A GLU* 2.8 42.0 + - - +
161A ILE* 4.4 4.9 - - + -
162A ALA* 1.3 77.9 - - - +
164A GLY* 1.3 67.4 + - - +
165A ARG 3.7 0.2 + - - -
173A MSE 4.0 3.1 - - - -
174A VAL* 2.8 36.5 + - + +
176A ARG* 2.9 45.2 - - + +
156D ILE 3.6 7.0 - - - +
157D THR* 4.3 6.7 - - - +
183D TYR* 6.1 1.3 - - - -
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Residues in contact with GLY 164 (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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163A ARG* 1.3 77.7 - - - +
165A ARG* 1.3 60.7 + - - -
166A ALA 4.0 0.7 + - - -
171A THR* 3.7 19.5 - - - -
172A MSE 3.4 7.0 - - - -
173A MSE 3.9 8.0 - - - +
155D ASN* 5.6 2.6 - - - +
156D ILE* 2.9 21.6 + - - -
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Residues in contact with ARG 165 (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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163A ARG 3.7 0.2 + - - -
164A GLY* 1.3 73.0 - - - -
166A ALA* 1.3 72.3 + - - +
167A LEU* 3.2 21.7 + - + +
171A THR* 3.5 3.6 - - - +
172A MSE 2.8 60.8 + - + +
174A VAL* 3.8 35.8 - - + +
177B ASN* 6.0 0.2 - - - +
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Residues in contact with ALA 166 (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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164A GLY 4.0 1.8 + - - -
165A ARG* 1.3 75.4 - - - +
167A LEU* 1.3 68.0 + - - +
170A GLY 4.0 3.1 - - - -
171A THR* 4.7 7.8 - - + +
148D ARG* 6.4 0.2 - - - +
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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