Contacts of the strand formed by residues 195 - 203 (chain A) in PDB entry 1LEC
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 ARG 195 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160A ARG* 4.9 5.1 + - - +
162A GLU* 3.0 35.9 + - - +
165A ASP* 3.6 17.2 + - - +
190A SER* 4.0 0.2 - - - -
191A TYR* 3.5 30.8 + - - +
194A GLY* 1.3 75.7 - - - -
196A ASP* 1.3 84.2 + - - +
197A TYR* 3.3 39.1 - - + +
198A ILE* 5.7 2.2 - - - +
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Residues in contact with ASP 196 (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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188A LEU* 4.1 16.2 - - + -
189A LEU 3.2 7.4 - - - +
190A SER* 3.0 28.0 + - - -
191A TYR 4.6 1.6 + - - +
194A GLY 4.7 3.2 - - - +
195A ARG* 1.3 104.2 + - - +
197A TYR* 1.3 62.5 + - - +
198A ILE* 4.4 14.1 - - + +
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Residues in contact with TYR 197 (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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146A ILE* 3.5 24.7 - - + -
159A THR* 4.8 4.9 - - + -
160A ARG 3.1 28.3 - - - -
161A TRP* 3.6 14.1 - + - -
162A GLU* 3.0 21.6 + - - +
165A ASP* 2.6 30.2 + - - +
187A VAL* 3.5 1.0 - - - +
188A LEU* 3.3 9.5 - - - +
189A LEU* 2.8 54.7 + - + +
191A TYR* 3.7 18.4 - + - -
195A ARG* 3.3 41.1 - - + +
196A ASP* 1.3 76.2 - - - +
198A ILE* 1.3 63.4 + - - +
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Residues in contact with ILE 198 (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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159A THR* 3.8 15.5 + - - +
186A THR* 5.1 5.4 - - + -
187A VAL 3.4 4.9 - - - +
188A LEU* 4.5 13.0 - - + -
195A ARG* 5.7 1.1 - - - +
196A ASP* 4.4 17.7 - - + +
197A TYR* 1.3 81.2 - - - +
199A LEU* 1.3 64.8 + - - +
200A SER* 4.7 11.9 - - - +
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Residues in contact with LEU 199 (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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146A ILE* 3.8 25.1 - - + +
147A GLY* 4.1 3.4 - - - -
148A ILE* 3.8 25.9 - - + +
157A ALA* 3.8 28.7 - - + +
158A THR* 3.5 27.6 - - - +
159A THR* 4.0 13.2 - - + +
185A LEU 3.9 0.9 - - - +
186A THR* 3.5 0.5 - - - -
187A VAL* 2.7 46.3 + - + +
198A ILE* 1.3 76.0 - - - +
200A SER* 1.3 66.1 + - - +
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Residues in contact with SER 200 (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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148A ILE* 4.4 1.1 - - - -
184A ILE* 4.7 6.5 - - - -
185A LEU 3.1 5.2 - - - -
186A THR* 2.8 36.3 + - - +
198A ILE* 4.3 7.8 - - - +
199A LEU* 1.3 81.6 - - - +
201A HIS* 1.3 67.3 + - - +
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Residues in contact with HIS 201 (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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148A ILE* 3.7 21.3 - - + -
156A VAL* 3.8 39.0 - - + +
157A ALA* 3.8 16.7 - - + +
184A ILE* 3.6 3.5 - - - +
185A LEU* 2.8 37.3 + - - +
200A SER* 1.3 79.4 + - - +
202A VAL* 1.3 91.6 + - + +
203A VAL* 3.4 6.2 + - + +
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Residues in contact with VAL 202 (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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182A SER 4.8 3.6 - - - +
183A LYS* 3.3 17.5 - - + +
184A ILE* 3.9 22.7 - - + +
201A HIS* 1.3 96.1 + - + +
203A VAL* 1.3 61.1 + - - +
204A ASP* 5.2 0.9 - - + +
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Residues in contact with VAL 203 (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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126A VAL* 4.7 2.0 - - + -
148A ILE* 5.1 3.6 - - + -
150A VAL* 3.8 35.7 - - + -
178A TYR* 3.1 22.7 - - + -
183A LYS* 2.6 14.5 + - - +
185A LEU* 3.6 38.1 - - + +
201A HIS* 4.0 7.0 - - + +
202A VAL* 1.3 76.8 - - - +
204A ASP* 1.3 62.0 + - - +
205A LEU* 3.4 24.6 + - + -
208A VAL* 4.6 4.5 - - + -
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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