Contacts of the strand formed by residues 193 - 198 (chain A) in PDB entry 1PTG
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 ASN 193 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185A THR* 4.1 11.3 + - - -
186A THR 2.9 29.1 + - - -
187A THR* 4.3 4.5 - - - +
188A VAL* 4.1 1.8 - - - -
192A ALA* 1.3 78.2 - - - +
194A VAL* 1.3 57.2 + - - +
226A ASN 3.6 8.2 + - - +
227A HIS* 3.7 29.9 + - + +
228A LEU* 2.7 35.6 + - - +
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Residues in contact with VAL 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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176A PHE* 3.9 39.0 - - + -
184A PHE* 3.9 1.7 - - + +
185A THR* 2.9 7.8 + - - -
186A THR* 2.8 45.8 + - - +
188A VAL* 3.2 24.7 - - + +
193A ASN* 1.3 72.4 - - - +
195A THR* 1.3 63.7 + - - +
196A VAL* 4.0 6.9 + - + -
228A LEU* 3.4 34.8 - - + +
230A ILE* 4.2 12.1 - - + -
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Residues in contact with THR 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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183A THR* 5.9 2.7 - - - +
184A PHE 3.3 11.4 - - - +
185A THR* 3.6 14.0 + - - -
194A VAL* 1.3 70.5 - - - +
196A VAL* 1.3 65.0 + - - +
214A THR* 4.2 14.6 - - + +
217A GLU* 3.8 21.6 + - - +
227A HIS* 2.8 24.6 + - - -
228A LEU 3.0 6.9 + - - -
229A TYR* 3.4 23.7 - - + +
230A ILE* 3.0 26.0 + - - +
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Residues in contact with VAL 196 (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 PHE* 4.4 1.3 - - + -
178A TRP* 4.0 20.0 - - + -
182A GLU 3.8 0.2 - - - +
183A THR* 2.9 6.5 - - - -
184A PHE* 2.9 72.0 + - + +
194A VAL* 4.0 10.7 - - + -
195A THR* 1.3 81.2 - - - +
197A GLN* 1.3 62.2 + - - +
198A ASP* 3.8 19.1 - - + -
230A ILE* 3.5 28.0 - - + +
232A PHE* 4.3 5.8 - - + -
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Residues in contact with GLN 197 (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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183A THR* 3.7 14.1 - - + -
196A VAL* 1.3 73.0 - - - +
198A ASP* 1.3 57.1 + - - +
199A LYS* 2.9 44.3 - - - +
207A LYS* 3.2 10.5 + - - +
210A SER* 3.6 21.2 - - - +
211A ILE* 3.7 12.5 - - - +
214A THR* 3.4 31.9 - - + +
230A ILE 3.1 13.7 + - - +
231A ASN* 3.9 6.7 - - - +
232A PHE* 2.7 49.0 + - - +
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Residues in contact with ASP 198 (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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178A TRP* 2.8 24.9 + - + +
179A PRO 5.3 1.0 - - - +
181A ASN* 3.4 8.2 + - - -
182A GLU 2.8 27.8 + - - +
184A PHE* 5.0 1.6 - - + -
196A VAL* 3.8 17.3 - - + -
197A GLN* 1.3 74.1 - - - +
199A LYS* 1.3 58.0 + - - +
200A TYR* 3.2 10.3 + - - +
207A LYS* 4.7 0.4 + - - -
232A PHE* 4.1 14.3 - - + +
801A INS 2.6 52.3 + - - -
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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