Contacts of the strand formed by residues 199 - 207 (chain A) in PDB entry 1A1A
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 GLY 199 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194A PHE* 3.2 20.2 - - - -
195A ASP 3.0 17.0 + - - -
197A ALA 3.3 3.6 - - - +
198A LYS* 1.3 77.7 - - - +
200A LEU* 1.3 64.1 + - - -
201A ASN* 2.9 22.2 + - - -
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Residues in contact with LEU 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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166A LEU* 3.3 44.0 - - + +
167A ASN 4.9 0.9 - - - +
168A ALA* 4.1 22.2 - - + -
170A ASN 5.5 6.5 - - - +
171A PRO 6.5 0.2 - - - -
172A ARG* 6.1 3.8 - - + +
192A SER* 6.1 4.5 - - - -
193A ASP 3.5 12.8 - - - +
194A PHE* 3.0 31.0 - - + -
198A LYS 3.9 4.3 - - - +
199A GLY* 1.3 72.3 - - - -
201A ASN* 1.3 61.2 + - - +
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Residues in contact with ASN 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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166A LEU* 3.7 7.5 - - - +
192A SER* 3.5 4.2 - - - -
193A ASP* 2.8 42.2 + - - +
194A PHE* 4.1 1.8 - - - +
195A ASP* 3.7 14.9 + - - +
198A LYS* 4.2 15.5 - - + +
199A GLY 2.9 22.5 + - - +
200A LEU* 1.3 76.1 - - - +
202A VAL* 1.3 66.8 + - - +
203A LYS* 2.9 34.1 + - - +
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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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162A GLU* 3.6 26.2 - - + +
165A LEU* 3.8 41.3 - - + -
166A LEU* 3.9 16.3 - - + +
190A SER* 4.0 0.2 - - - -
191A VAL 3.3 11.0 - - - +
192A SER* 4.4 2.7 - - - -
201A ASN* 1.3 84.6 - - - +
203A LYS* 1.3 72.3 + - - +
204A HIS* 3.5 35.2 + - + -
102C GLU* 5.4 0.3 - - - +
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Residues in contact with LYS 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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189A LEU 3.5 1.4 - - - +
190A SER* 3.2 3.8 - - - -
191A VAL* 2.8 35.8 + - - +
193A ASP* 3.2 28.7 - - + -
195A ASP* 5.5 2.0 + - - -
201A ASN* 2.9 23.2 + - - +
202A VAL* 1.3 75.3 - - - +
204A HIS* 1.3 61.2 + - - +
205A TYR* 3.9 15.8 - - + +
241A CYS* 3.4 24.7 - - + -
102C GLU* 3.7 36.9 + - + +
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Residues in contact with HIS 204 (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 ARG* 3.5 38.7 + - + +
161A SER* 3.8 14.4 - - - -
162A GLU* 2.7 35.6 + - + -
178A ARG* 3.3 9.4 + - - -
189A LEU 3.5 3.6 - - - -
190A SER* 3.0 18.4 + - - -
202A VAL* 3.5 27.7 + - + +
203A LYS* 1.3 76.4 - - - +
205A TYR* 1.3 57.8 + - - +
100C ACE 3.8 6.6 + - - +
101C PTH 2.9 21.9 - - + +
102C GLU* 2.9 30.3 + - - +
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Residues in contact with TYR 205 (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 SER* 3.3 1.9 - - - -
189A LEU* 2.8 47.6 + - + +
191A VAL* 3.9 23.3 - - + -
203A LYS* 3.9 16.5 - - + +
204A HIS* 1.3 71.3 - - - +
206A LYS* 1.3 64.2 + - - +
207A ILE 3.5 0.2 + - - -
217A ILE* 4.0 28.7 - - + -
239A GLY 4.6 0.7 + - - -
240A LEU* 3.6 34.0 - - + -
241A CYS* 2.8 34.7 + - - +
101C PTH 3.3 2.6 + - - -
102C GLU* 3.4 35.7 + - + +
103C DIP 4.3 15.9 - - + -
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Residues in contact with LYS 206 (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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180A SER* 3.4 7.0 + - - +
182A THR* 4.0 0.8 + - - -
183A THR* 2.6 25.4 + - - +
186A ALA* 3.5 27.8 - - + -
187A TYR 3.4 5.4 - - - +
188A SER* 4.0 3.4 - - - -
205A TYR* 1.3 75.7 - - - +
207A ILE* 1.3 63.1 + - - +
208A ARG* 3.8 37.3 - - + +
216A TYR 4.0 0.5 - - - +
217A ILE* 3.6 22.0 - - - +
160B GLU* 5.2 0.6 + - - -
101C PTH 3.1 52.8 - - + +
102C GLU 5.2 2.2 + - - -
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Residues in contact with ILE 207 (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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177A VAL* 4.0 18.6 - - + -
186A ALA* 3.4 6.1 - - - +
187A TYR* 2.7 43.8 + - + +
189A LEU* 4.0 21.3 - - + +
205A TYR 4.2 3.8 - - - +
206A LYS* 1.3 75.8 - - - +
208A ARG* 1.3 63.4 + - - +
215A PHE* 3.8 22.9 - - + -
216A TYR 3.4 6.3 - - - +
217A ILE* 3.8 18.2 - - + -
226A LEU* 3.8 25.6 - - + -
229A LEU* 3.7 29.6 - - + -
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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