Contacts of the strand formed by residues 198 - 204 (chain A) in PDB entry 1P4V
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 198 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164A LEU* 3.4 16.1 - - - +
193A VAL* 3.7 0.3 - - - -
194A ASP* 2.9 32.0 + - - +
197A ILE* 1.3 79.8 - - - +
199A ALA* 1.3 61.3 + - - -
219A VAL* 3.9 5.9 - - - +
222A MET* 4.1 9.2 - - - -
260A LEU 3.0 13.7 - - - -
261A ASN* 3.8 1.1 - - - -
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Residues in contact with ALA 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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156A ILE* 3.6 21.8 - - + +
164A LEU* 4.3 13.0 - - + +
165A SER 4.9 1.1 - - - +
192A PHE 3.3 5.8 - - - -
193A VAL* 3.7 29.6 - - + -
198A GLY* 1.3 74.8 - - - +
200A ALA* 1.3 60.9 - - - +
219A VAL* 4.0 3.6 - - - -
222A MET* 3.7 2.0 - - - +
259A ALA* 3.2 4.0 - - - +
260A LEU* 2.8 32.3 + - + +
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Residues in contact with ALA 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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156A ILE* 4.1 4.5 - - - -
191A LEU* 3.5 2.8 - - - +
192A PHE 3.0 31.6 + - - +
199A ALA* 1.3 77.9 - - - +
201A THR* 1.3 62.6 + - - +
215A THR* 3.3 12.3 - - + +
218A VAL* 3.7 35.4 - - + -
219A VAL* 4.0 8.7 - - + +
257A PHE* 5.3 1.3 - - + -
258A ILE 3.3 12.8 - - - +
259A ALA* 4.1 0.2 - - + -
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Residues in contact with THR 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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10A THR* 4.2 3.9 - - + +
154A GLY* 3.6 34.4 - - - -
155A MET 4.0 1.7 + - - +
156A ILE* 4.0 7.9 - - + -
168A CYS* 4.1 7.1 - - - +
190A GLY 2.8 18.8 + - - -
191A LEU* 4.0 15.0 - - - +
200A ALA* 1.3 76.9 - - - +
202A ALA* 1.3 60.6 + - - +
215A THR* 3.5 4.3 - - - -
257A PHE* 3.5 2.8 - - - +
258A ILE* 3.1 56.5 + - + +
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Residues in contact with ALA 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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10A THR* 4.2 11.2 + - - +
152A THR* 5.4 7.3 - - - +
154A GLY* 5.2 2.1 + - - -
168A CYS* 5.2 6.2 - - - -
183A ASP* 3.9 13.7 - - - +
189A ALA 4.0 4.7 - - - +
190A GLY 2.9 10.1 + - - +
201A THR* 1.3 78.4 + - - +
203A THR* 1.3 61.5 + - - +
209A VAL* 3.8 24.2 - - + -
256A GLY 3.5 4.9 - - - +
257A PHE* 3.6 26.5 - - + -
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Residues in contact with THR 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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10A THR* 4.6 2.9 - - - -
11A TRP* 3.3 32.4 + - - +
145A VAL* 4.4 0.5 - - - +
152A THR* 6.1 4.3 - - - -
183A ASP* 5.7 0.4 - - - -
202A ALA* 1.3 77.7 - - - +
204A GLY* 1.3 63.8 + - - +
209A VAL* 4.2 5.9 - - - +
254A GLN* 5.4 4.0 - - + -
255A VAL* 3.7 2.9 - - - -
256A GLY* 3.1 44.7 + - - +
257A PHE* 4.9 0.4 - - - -
270A CYS* 4.3 1.3 - - - -
275A PHE* 3.3 39.8 - - + -
296A GLY 5.5 0.4 - - - -
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Residues in contact with GLY 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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145A VAL* 3.8 26.1 - - - +
150A HIS 5.7 1.2 + - - -
173A MET* 4.4 1.2 - - - +
183A ASP* 4.4 0.3 - - - +
203A THR* 1.3 81.0 + - - +
205A HIS* 1.3 67.9 + - - -
206A GLY* 3.0 4.5 + - - -
209A VAL* 4.8 2.4 - - - +
254A GLN* 3.2 14.1 - - - -
296A GLY* 3.2 19.1 + - - +
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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