Contacts of the strand formed by residues 184 - 193 (chain A) in PDB entry 1LCY
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 184 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A PHE* 3.9 22.2 - - + -
110A LEU* 3.7 35.9 - - + -
111A PRO 2.8 19.8 + - - +
112A LEU* 3.5 12.8 - - + -
113A GLY 2.7 23.7 + - - -
176A PRO* 3.8 15.9 - - + -
177A LEU 3.7 3.8 - - - +
178A VAL* 4.5 2.7 - - + +
183A GLU* 1.3 72.3 - - - +
185A ILE* 1.3 57.3 + - - +
186A GLY 3.3 29.6 - - - +
202A SER* 3.2 11.6 - - - -
205A LEU* 5.0 1.3 - - + -
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Residues in contact with ILE 185 (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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113A GLY* 4.4 14.4 - - - -
114A ARG 4.7 2.5 - - - +
115A SER* 3.7 1.7 - - - -
118A VAL* 3.7 29.6 - - + -
124A VAL* 4.3 12.8 - - + -
142A VAL* 5.1 1.3 - - + -
162A ILE* 2.8 41.0 - - + +
177A LEU* 3.0 43.3 + - + +
179A ASN* 3.6 37.2 - - + +
183A GLU 3.4 0.6 + - - +
184A VAL* 1.3 77.5 - - - +
186A GLY* 1.3 57.9 + - - +
202A SER* 3.0 23.6 + - - +
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Residues in contact with GLY 186 (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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162A ILE* 4.4 2.5 - - - -
176A PRO* 3.5 0.9 - - - +
177A LEU* 2.8 37.9 + - - -
184A VAL* 3.3 15.2 - - - +
185A ILE* 1.3 83.9 - - - +
187A VAL* 1.3 62.1 + - - -
199A ALA* 4.4 2.5 - - - -
200A ILE 2.8 14.6 - - - -
202A SER* 4.0 2.7 - - - -
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Residues in contact with VAL 187 (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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52A PHE* 4.2 6.7 - - + -
61A VAL* 4.1 9.4 - - + -
62A THR 4.4 11.0 - - - +
63A ASN* 3.8 19.1 - - - +
96A ILE* 4.4 11.9 - - + -
174A GLY* 3.8 22.9 - - - +
175A GLY 3.7 2.5 - - - +
176A PRO* 4.6 0.4 - - - -
186A GLY* 1.3 75.1 - - - +
188A ASN* 1.3 70.2 + - - +
189A THR* 2.8 15.9 + - - -
199A ALA* 3.2 2.5 - - - -
200A ILE* 2.8 33.5 + - + +
205A LEU* 3.8 30.5 - - + -
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Residues in contact with ASN 188 (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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63A ASN* 2.8 5.5 + - - +
126A ALA* 3.7 7.0 - - - +
127A MET 3.0 33.3 + - - +
168A ILE* 3.5 31.2 - - + +
172A ASN* 3.1 21.5 + - - +
173A ALA* 4.1 0.9 - - - -
174A GLY 2.8 26.1 + - - -
175A GLY 2.8 17.4 + - - +
176A PRO 3.3 6.5 + - - -
177A LEU* 3.3 28.9 + - - +
186A GLY 4.0 0.2 - - - -
187A VAL* 1.3 70.5 - - - +
189A THR* 1.3 59.3 + - - +
199A ALA* 4.0 1.3 - - - -
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Residues in contact with THR 189 (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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63A ASN* 3.5 7.8 + - - +
65A HIS* 3.8 8.8 - - - -
95A ASP* 3.4 31.4 - - + +
161A TYR* 4.6 9.9 - - + -
168A ILE* 3.9 4.4 - - - +
173A ALA* 3.9 8.7 - - - +
187A VAL 2.8 14.2 + - - -
188A ASN* 1.3 73.8 - - - +
190A MET* 1.3 83.8 + - + +
198A PHE 2.9 19.9 + - - -
199A ALA* 4.4 0.2 - - - -
200A ILE* 3.1 20.0 + - - +
232A MET* 3.7 9.9 - - + +
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Residues in contact with MET 190 (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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95A ASP* 5.2 1.6 - - + +
161A TYR* 4.5 12.6 - - + +
168A ILE* 3.8 11.1 - - - +
169A ASP* 6.1 0.7 - - - +
189A THR* 1.3 91.8 - - + +
191A LYS* 1.3 58.9 + - - +
192A VAL* 3.6 6.7 + - + -
197A SER* 3.3 2.6 - - - -
198A PHE* 2.7 47.1 + - + +
232A MET* 3.9 20.0 - - + -
233A MET 3.8 23.3 - - - +
234A LEU* 4.2 29.2 - - + -
261A HIS* 3.6 38.8 - - + +
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Residues in contact with LYS 191 (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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167A ALA* 3.4 35.3 - - - +
168A ILE 3.0 28.9 + - - +
169A ASP* 4.5 12.5 - - + +
190A MET* 1.3 72.8 - - - +
192A VAL* 1.3 66.1 + - - +
193A THR* 3.8 23.8 + - - +
194A ALA* 5.1 4.0 - - - +
195A GLY 5.6 3.8 - - - +
196A ILE 3.8 3.8 - - - +
197A SER* 3.9 5.0 + - - +
261A HIS* 3.7 21.2 + - - +
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Residues in contact with VAL 192 (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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190A MET* 3.6 6.3 + - + +
191A LYS* 1.3 75.1 - - - +
193A THR* 1.3 74.1 + - - +
196A ILE* 2.8 25.2 + - + +
198A PHE* 3.5 52.0 - - + -
234A LEU* 4.0 20.9 - - + -
240A ILE* 4.6 11.0 - - + +
243A GLU* 5.9 2.5 - - + +
244A LEU* 4.1 18.4 - - + +
261A HIS* 5.9 1.6 - - - -
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Residues in contact with THR 193 (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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191A LYS* 3.5 14.2 - - - +
192A VAL* 1.3 91.4 + - - +
194A ALA* 1.3 75.1 + - + +
195A GLY 3.0 0.9 + - - -
196A ILE* 2.8 32.9 + - - +
244A LEU* 3.0 25.8 - - + +
247A ARG* 3.9 44.9 - - + +
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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