Contacts of the strand formed by residues 204 - 209 (chain A) in PDB entry 1TW2
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 SER 204 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180A ARG 3.2 10.0 + - - -
181A HIS* 3.4 21.1 - - - -
182A VAL 3.0 21.1 + - - -
202A HIS 4.1 1.8 + - - -
203A VAL* 1.3 79.8 + - - +
205A ALA* 1.3 63.3 + - - +
228A ASP 5.1 1.7 + - - -
229A ARG* 3.4 18.8 + - - +
230A VAL* 5.5 0.2 - - - -
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Residues in contact with ALA 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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181A HIS* 3.6 5.6 + - - -
182A VAL* 3.1 23.1 - - + +
184A ASP* 6.3 0.2 - - + -
193A ALA* 4.2 20.9 - - + +
196A ILE* 6.4 0.9 - - + -
197A ALA* 6.3 0.4 - - + -
203A VAL* 5.2 2.5 - - + -
204A SER* 1.3 77.9 - - - +
206A THR* 1.3 66.2 + - - +
229A ARG 2.9 8.3 + - - +
230A VAL* 3.3 20.0 - - + -
231A ASP* 3.0 25.9 + - - +
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Residues in contact with THR 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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181A HIS* 3.0 25.0 + - - -
182A VAL 2.9 6.5 + - - -
183A LEU* 3.4 21.6 - - + +
184A ASP* 2.7 33.3 + - - +
205A ALA* 1.3 73.9 + - - +
207A VAL* 1.3 61.7 - - - +
231A ASP* 3.5 14.5 + - + +
233A VAL* 4.0 27.8 - - + -
242A PRO* 4.7 8.3 - - + -
243A ARG* 4.0 11.2 - - + -
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Residues in contact with VAL 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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184A ASP* 3.6 14.4 - - + +
187A GLY* 4.2 13.0 - - - +
188A GLY 4.1 19.7 - - - +
190A GLY* 4.2 13.7 - - - -
193A ALA* 3.9 27.4 - - + -
206A THR* 1.3 77.5 - - - +
208A LEU* 1.3 66.8 + - - +
209A GLU* 4.3 4.5 - - + -
217A ALA* 4.9 1.8 - - + -
221A LEU* 4.5 3.6 - - + -
230A VAL* 4.0 8.7 - - + -
231A ASP 2.9 15.5 + - - +
232A VAL* 3.4 13.4 - - + +
233A VAL* 2.8 29.8 + - - +
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Residues in contact with LEU 208 (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 LEU* 4.6 9.6 - - + -
184A ASP 3.1 10.5 + - - +
185A VAL* 4.4 11.9 - - + -
186A GLY* 2.8 31.8 + - - +
187A GLY 3.4 0.7 + - - -
206A THR 4.1 0.8 + - - -
207A VAL* 1.3 71.6 - - - +
209A GLU* 1.3 62.6 + - - +
233A VAL* 3.4 26.2 - - + +
234A GLU 4.1 1.3 - - - -
235A GLY* 3.7 27.4 - - - +
236A ASP 4.2 4.9 - - - +
237A PHE* 4.1 27.8 - - + +
241A LEU* 4.1 12.3 - - + -
242A PRO* 4.0 24.5 - - + -
635A SAH 4.8 5.1 - - + -
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Residues in contact with GLU 209 (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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186A GLY* 3.0 14.2 - - - +
187A GLY 3.7 1.1 - - - +
188A GLY 3.0 40.6 + - - +
207A VAL* 4.1 6.6 + - + -
208A LEU* 1.3 77.6 - - - +
210A MET* 1.3 73.7 + - - +
213A THR* 3.6 16.1 - - + +
214A VAL* 3.4 24.3 - - + +
233A VAL 3.2 6.1 + - - -
234A GLU* 3.4 0.3 - - - -
235A GLY 3.2 26.0 + - - -
635A SAH 2.3 53.3 + - - -
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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