Contacts of the strand formed by residues 243 - 252 (chain A) in PDB entry 4X6D
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 243 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A ASP* 3.7 33.4 - - + -
210A GLY 2.7 31.0 + - - -
211A PHE* 2.9 45.9 + - + +
212A TYR* 4.8 6.5 - + - -
213A PRO 4.4 0.7 - - - -
214A LYS* 3.3 55.3 - - + +
235A ILE* 3.5 26.7 - - + -
236A LEU 3.3 22.0 - - - -
237A PRO* 3.5 31.9 - - + -
238A SER* 5.8 0.9 - - - -
241A GLY 3.9 13.6 + - - -
242A THR* 1.3 77.7 - - - +
244A TYR* 1.3 58.2 + - - +
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Residues in contact with TYR 244 (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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190A TRP* 3.8 25.5 - + - -
207A HIS* 2.5 34.1 + - + -
208A VAL 3.4 10.5 - - - -
209A SER* 3.3 22.7 - - - -
210A GLY 4.8 0.9 - - - +
211A PHE* 4.2 0.9 - - - -
234A ASP 3.7 1.0 - - - +
235A ILE* 3.6 2.4 - - - -
236A LEU* 2.7 50.1 + - + +
238A SER* 5.3 3.8 - - - +
243A TRP* 1.3 76.4 - - - +
245A LEU* 1.3 66.2 + - - +
246A ARG* 2.9 38.4 + - + +
10B TYR* 3.7 34.9 - + + +
11B SER 4.8 9.6 - - - +
12B ARG* 5.2 0.4 - - - -
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Residues in contact with LEU 245 (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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206A CYS 3.7 1.7 - - - +
207A HIS* 3.9 1.2 - - - -
208A VAL* 2.8 40.3 + - + +
211A PHE* 4.2 11.4 - - + -
216A VAL* 3.6 27.8 - - + -
218A VAL* 4.3 17.1 - - + +
232A ARG* 3.8 24.9 - - + +
233A GLY 3.3 30.7 - - - +
234A ASP 3.3 15.5 - - - +
235A ILE* 4.1 8.1 - - + +
244A TYR* 1.3 82.5 - - - +
246A ARG* 1.3 74.7 + - - +
247A ALA* 5.7 0.4 - - + -
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Residues in contact with ARG 246 (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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205A VAL* 3.7 16.4 - - + -
206A CYS 3.4 3.4 - - - +
207A HIS* 3.4 25.8 - - + +
231A GLN 3.9 0.7 - - - +
232A ARG* 4.0 0.2 - - - -
233A GLY* 2.9 31.3 + - - -
234A ASP 4.7 1.6 + - - -
236A LEU* 5.1 10.9 - - - +
244A TYR* 2.9 45.5 + - + +
245A LEU* 1.3 79.2 - - - +
247A ALA* 1.3 59.8 + - - +
248A THR* 4.2 8.2 - - + +
8B GLN* 5.4 6.7 + - - +
9B VAL 5.0 8.3 + - - -
10B TYR* 4.6 9.3 - - - +
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Residues in contact with ALA 247 (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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206A CYS* 3.0 24.0 + - + -
218A VAL* 3.5 42.1 - - + +
220A TRP* 3.0 18.3 + - + +
230A THR* 4.4 10.8 - - + -
231A GLN 3.4 9.0 - - - +
232A ARG* 4.8 4.5 - - + -
245A LEU* 4.2 2.2 - - + -
246A ARG* 1.3 74.0 - - - +
248A THR* 1.3 62.8 + - - +
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Residues in contact with THR 248 (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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203A GLN* 3.2 30.0 + - - +
204A LEU 3.2 6.3 - - - -
205A VAL* 3.8 26.2 - - + -
220A TRP* 3.9 2.6 - - - -
229A GLY 3.8 0.2 - - - +
230A THR* 3.4 5.0 - - - -
231A GLN* 2.8 55.0 + - - +
246A ARG* 4.8 8.5 - - + -
247A ALA* 1.3 79.9 - - - +
249A LEU* 1.3 61.4 + - - +
250A GLU* 6.0 1.1 - - - +
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Residues in contact with LEU 249 (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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202A LEU 3.7 0.3 - - - +
203A GLN* 3.5 1.8 - - - -
204A LEU* 2.9 34.6 + - + +
220A TRP* 3.6 34.8 - - + +
227A GLN* 4.4 15.0 - - + +
228A GLN 4.1 8.3 - - - +
229A GLY* 3.8 8.3 - - - +
230A THR* 3.7 27.1 - - - +
248A THR* 1.3 76.5 - - - +
250A GLU* 1.3 71.4 + - - +
251A VAL* 3.6 24.6 + - + -
259A LEU* 3.6 18.8 - - + -
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Residues in contact with GLU 250 (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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197A PRO* 3.3 35.4 - - + +
201A HIS* 5.6 4.0 - - + -
202A LEU 3.3 6.3 - - - +
203A GLN* 4.3 19.0 + - + -
229A GLY 5.1 1.6 + - - -
231A GLN* 5.7 3.3 + - - +
248A THR* 6.0 1.1 - - - +
249A LEU* 1.3 84.9 - - - +
251A VAL* 1.3 64.4 + - - +
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Residues in contact with VAL 251 (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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201A HIS* 3.2 11.0 - - - +
202A LEU* 2.8 42.1 + - + -
204A LEU* 4.3 13.5 - - + -
227A GLN* 5.9 0.7 - - - +
249A LEU* 3.6 31.6 - - + +
250A GLU* 1.3 81.5 - - - +
252A ALA* 1.3 71.9 + - - +
255A GLU* 4.1 15.3 - - + +
256A ALA* 4.1 22.0 - - + -
259A LEU* 3.6 12.8 - - + -
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Residues in contact with ALA 252 (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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200A GLY 3.6 7.6 - - - +
201A HIS* 3.8 21.8 - - + +
251A VAL* 1.3 86.3 - - - +
253A ALA* 1.3 67.7 + - - +
254A GLY 3.2 2.9 - - - +
255A GLU* 3.1 34.2 + - + +
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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