Contacts of the strand formed by residues 187 - 195 (chain A) in PDB entry 1A1C
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 TYR 187 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146A ILE* 5.6 4.5 - - + +
152A TYR* 3.5 35.9 + + - -
177A VAL* 4.3 8.5 - - + -
178A ARG 3.2 18.4 - - - +
179A GLU* 4.2 11.0 + - + +
180A SER* 4.0 2.8 - - - +
185A GLY 4.3 12.6 - - - -
186A ALA* 1.3 78.0 - - - +
188A CYS* 1.3 65.7 + - - +
206A LYS* 3.6 7.4 - - - +
207A ILE* 2.9 41.9 + - + +
209A LYS* 5.3 4.3 - - + -
215A PHE* 3.9 30.7 - + - -
226A LEU* 4.3 17.5 - - + -
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Residues in contact with CYS 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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176A LEU 3.8 0.5 - - - +
177A VAL* 3.1 6.1 - - - +
178A ARG* 2.8 71.8 + - - +
180A SER* 4.5 5.8 - - - -
187A TYR* 1.3 79.1 - - - +
189A LEU* 1.3 61.8 + - - +
190A SER* 3.6 11.9 - - - -
204A HIS* 3.8 11.2 - - - -
205A TYR 3.5 7.4 - - - -
207A ILE* 4.1 5.4 - - - +
101C PTR 3.6 26.0 - - + -
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Residues in contact with LEU 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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175A PHE* 3.8 29.8 - - + -
176A LEU 3.4 13.2 - - - +
177A VAL* 4.2 9.6 - - + +
188A CYS* 1.3 71.8 - - - +
190A SER* 1.3 58.9 + - - +
191A VAL* 3.8 11.2 - - + -
204A HIS* 3.5 1.6 - - - -
205A TYR* 2.9 41.5 + - + +
207A ILE* 3.9 14.1 - - + +
217A ILE* 3.7 25.1 - - + -
229A LEU* 4.8 6.3 - - + -
230A VAL* 5.7 0.9 - - + -
233A TYR* 5.2 0.7 - - + -
240A LEU* 3.9 22.4 - - + -
244A LEU* 4.2 14.4 - - + -
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Residues in contact with SER 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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161A SER* 4.2 2.0 - - - -
165A LEU* 3.8 21.6 - - - +
175A PHE* 3.1 7.1 - - - +
176A LEU* 2.8 44.2 + - - +
178A ARG* 3.5 16.1 + - - -
188A CYS* 3.6 3.2 - - - -
189A LEU* 1.3 73.0 - - - +
191A VAL* 1.3 59.8 + - - +
203A LYS 3.7 5.2 - - - -
204A HIS* 2.8 30.3 + - - -
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Residues in contact with VAL 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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165A LEU* 4.6 0.9 - - - -
173A GLY* 3.9 19.7 - - - -
174A THR 3.4 5.6 - - - +
175A PHE* 4.3 0.2 - - + -
189A LEU* 3.8 23.1 - - + -
190A SER* 1.3 78.6 - - - +
192A SER* 1.4 72.5 + - - +
193A ASP* 3.9 0.9 + - - +
202A VAL* 3.4 6.5 - - - +
203A LYS* 3.0 32.4 + - - +
205A TYR* 4.0 16.2 - - + -
240A LEU* 5.1 3.1 - - + -
241A CYS* 4.0 20.6 - - - -
242A HIS* 4.3 9.9 - - + +
244A LEU* 4.1 16.4 - - + -
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Residues in contact with SER 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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165A LEU* 3.9 32.0 + - - +
166A LEU* 5.7 1.3 - - - -
170A ASN* 4.4 1.9 - - - +
171A PRO 3.0 23.2 + - - -
172A ARG* 3.6 1.6 - - - +
173A GLY 2.9 26.4 + - - -
174A THR* 2.9 23.5 + - - -
191A VAL* 1.4 75.8 - - - +
193A ASP* 1.3 65.6 + - - +
200A LEU* 5.7 5.6 - - - -
201A ASN 3.6 7.0 - - - -
202A VAL* 4.5 2.7 - - - -
241A CYS* 4.8 0.5 - - - -
242A HIS* 4.9 1.0 - - - +
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Residues in contact with ASP 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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172A ARG* 4.5 12.2 - - - -
192A SER* 1.3 78.9 - - - +
194A PHE* 1.3 79.9 + - - +
195A ASP* 5.6 2.1 - - - +
200A LEU* 3.4 11.0 - - - +
201A ASN* 2.9 41.5 + - - +
203A LYS* 2.5 31.2 + - + +
241A CYS* 3.8 29.4 - - - +
242A HIS* 4.8 4.5 - - - +
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Residues in contact with PHE 194 (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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172A ARG* 4.0 43.0 + - + +
193A ASP* 1.3 88.9 + - - +
195A ASP* 1.4 72.0 - - - +
196A ASN* 3.6 28.3 - - + -
199A GLY* 3.1 37.2 - - - -
200A LEU* 3.9 14.1 - - + -
201A ASN* 4.2 1.1 - - - -
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Residues in contact with ASP 195 (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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193A ASP* 5.6 2.5 - - - +
194A PHE* 1.4 80.5 - - - +
196A ASN* 1.3 56.3 + - - +
197A ALA* 3.0 17.7 + - - +
198A LYS* 2.9 33.7 + - - +
199A GLY 2.7 34.2 + - - -
201A ASN* 3.1 23.2 + - - +
203A LYS* 5.5 1.3 + - - +
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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