Contacts of the strand formed by residues 199 - 204 (chain A) in PDB entry 6ABP
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 TRP 199 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130A TRP* 3.5 6.0 - - - -
136A ALA* 3.5 27.6 - - + -
137A VAL 3.8 13.2 - - - -
138A MET* 3.7 30.3 - - + -
170A TYR* 4.0 14.6 - + - -
189A MET* 4.5 8.5 - - + -
190A LEU* 3.3 35.9 - - + +
193A HIS* 3.7 36.2 + + + -
196A VAL* 3.5 19.1 - - + +
198A HIS* 1.3 73.6 - - - +
200A LEU* 1.3 57.4 - - - +
201A ILE* 4.1 10.0 + - + -
216A THR* 4.9 1.3 - - + -
221A PHE* 3.4 34.1 - + - -
225A ASP 3.0 7.5 + - - -
226A ILE* 3.3 19.4 - - + +
227A ILE 2.9 29.6 + - - +
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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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121A LEU* 4.1 26.9 - - + +
122A TYR 4.9 0.2 - - - +
125A MET* 4.2 12.6 - - + -
130A TRP* 3.5 27.1 - - + -
135A SER* 5.9 0.4 - - - -
136A ALA 3.0 13.8 + - - +
137A VAL* 3.3 19.9 - - + -
138A MET* 2.7 32.4 + - - +
159A LEU* 3.8 28.9 - - + -
164A PHE* 4.2 13.7 - - + -
199A TRP* 1.3 72.5 - - - +
201A ILE* 1.4 58.7 - - - +
202A VAL 4.0 0.4 + - - -
227A ILE* 3.4 27.4 - - + +
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Residues in contact with ILE 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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117A GLN* 5.2 0.2 - - - -
121A LEU* 4.2 6.8 - - - +
138A MET* 3.4 19.7 - - + +
140A ILE* 4.1 23.3 - - + -
199A TRP* 4.4 9.0 - - + -
200A LEU* 1.4 76.8 - - - +
202A VAL* 1.3 64.1 + - - +
203A GLY 4.1 0.9 + - - -
209A VAL* 4.0 29.9 - - + +
212A GLY* 3.7 14.8 - - - -
213A VAL* 3.8 6.3 - - + +
216A THR* 3.6 20.4 - - + -
226A ILE* 3.5 30.7 - - + -
227A ILE 2.8 14.7 + - - +
228A GLY* 3.9 15.8 - - - -
229A ILE 4.2 5.4 + - - +
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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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117A GLN* 3.6 14.4 - - - +
121A LEU* 3.5 28.0 - - + -
137A VAL* 3.8 22.2 - - + -
138A MET 2.8 14.5 + - - +
139A ALA* 4.1 11.2 - - + -
140A ILE* 2.8 32.2 + - - +
152A THR* 4.2 21.8 - - + +
155A SER* 3.6 22.2 - - - +
156A MET* 4.8 2.2 - - + -
159A LEU* 3.9 6.3 - - + -
200A LEU 5.1 0.2 - - - +
201A ILE* 1.3 74.8 - - - +
203A GLY* 1.3 63.8 + - - +
209A VAL* 4.4 1.8 - - - -
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Residues in contact with GLY 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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117A GLN* 3.0 24.5 + - - +
140A ILE 3.8 12.8 - - - -
151A ARG* 5.6 0.4 - - - +
152A THR* 3.8 7.2 - - - -
202A VAL* 1.3 77.4 - - - +
204A MET* 1.3 62.8 + - - -
205A ASN 3.3 3.4 + - - -
208A THR* 3.8 14.4 - - - -
209A VAL* 3.7 14.2 - - - +
231A ILE* 4.5 0.5 - - - +
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Residues in contact with MET 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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140A ILE 4.5 1.3 + - - +
142A ALA* 5.4 2.9 - - + +
145A LEU* 4.1 4.7 - - + -
148A ALA* 3.7 47.8 - - + +
151A ARG* 2.9 62.3 + - + +
152A THR* 3.7 9.8 - - + +
177A ASN* 3.6 38.4 - - + +
203A GLY* 1.3 72.6 - - - -
205A ASN* 1.3 81.2 + - - +
208A THR* 4.4 9.5 - - + +
231A ILE* 3.4 8.6 - - - +
307A ARA 4.0 12.6 - - - +
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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