Contacts of the strand formed by residues 201 - 215 (chain J) in PDB entry 4XLN
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 201 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184J GLU* 4.1 6.3 - - - -
185J VAL 2.9 28.5 + - - -
200J ASP* 1.3 79.7 - - - +
202J VAL* 1.3 65.1 + - - -
203J ALA 3.4 0.9 + - - -
395J VAL* 3.4 8.3 - - - +
396J VAL 3.5 8.1 - - - -
397J LYS* 4.1 7.9 - - - -
398J ALA 4.4 5.8 - - - -
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Residues in contact with VAL 202 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182J GLY* 3.9 28.3 - - - +
183J GLU 4.2 1.3 - - - +
184J GLU* 3.6 26.9 - - + +
201J GLY* 1.3 68.6 - - - -
203J ALA* 1.3 61.5 + - - +
204J LEU* 3.5 21.5 - - + +
396J VAL 2.9 34.0 + - - +
398J ALA* 3.9 29.4 - - + +
400J VAL* 3.7 33.9 - - + +
445J ARG* 5.5 1.1 - - + -
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Residues in contact with ALA 203 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179J VAL* 4.9 10.3 - - + -
180J LYS 4.2 4.0 - - - +
182J GLY 3.3 20.4 + - - -
183J GLU 3.3 13.8 + - - +
185J VAL* 3.6 25.4 - - + -
191J LEU* 5.1 7.6 - - + -
201J GLY 3.4 1.0 + - - -
202J VAL* 1.3 73.3 - - - +
204J LEU* 1.3 63.2 + - - +
205J TYR* 6.0 0.4 - - - -
393J ILE* 5.9 4.5 - - + -
394J LEU 3.7 6.1 - - - +
395J VAL* 3.7 17.3 - - + +
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Residues in contact with LEU 204 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181J ASP* 3.4 13.5 - - - +
182J GLY* 3.4 14.6 - - - +
202J VAL* 3.5 29.2 - - + +
203J ALA* 1.3 81.7 - - - +
205J TYR* 1.3 66.2 + - - +
206J ARG* 3.9 6.4 - - - +
393J ILE* 3.5 7.3 - - - +
394J LEU* 2.9 40.5 + - + +
396J VAL* 4.7 11.0 - - + -
400J VAL* 6.1 0.2 - - + -
441J ARG* 3.4 35.7 - - - +
445J ARG* 4.6 17.7 - - + +
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Residues in contact with TYR 205 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176J ASP* 4.5 0.9 + - - -
177J ALA* 4.2 10.8 + - + +
179J VAL* 2.8 44.3 + - + +
180J LYS* 4.0 13.2 - - - +
181J ASP* 2.8 27.8 + - + +
203J ALA 5.7 0.2 - - - -
204J LEU* 1.3 77.4 - - - +
206J ARG* 1.3 69.4 + - - +
207J PHE 4.1 0.8 + - - -
208J PRO* 4.5 13.0 - - + -
357J GLU* 4.2 2.7 - - - -
387J LEU* 3.3 49.1 + - + -
388J HIS* 4.0 7.6 + - - -
390J PRO* 3.6 28.4 - - + +
393J ILE* 3.4 14.8 - - + -
441J ARG* 5.3 2.9 + - - -
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Residues in contact with ARG 206 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168J THR* 4.9 8.6 - - + +
204J LEU* 4.1 8.5 - - - -
205J TYR* 1.3 85.3 - - - +
207J PHE* 1.3 87.2 - - + +
208J PRO 3.8 0.2 - - - -
390J PRO* 4.0 1.0 - - - +
391J ALA* 3.1 1.7 + - - +
392J SER* 2.9 55.3 + - - +
393J ILE* 3.9 1.6 - - - -
394J LEU* 3.3 50.7 - - + +
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Residues in contact with PHE 207 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205J TYR 4.1 0.6 + - - -
206J ARG* 1.3 93.0 - - + +
208J PRO* 1.3 72.0 - - - +
209J ARG* 3.5 3.5 + - - +
351J MET 5.8 5.2 - - - -
391J ALA* 2.7 40.2 + - + +
112L GLU* 3.5 48.9 - - + +
113L GLU* 3.8 20.2 - - + -
116L ASP* 3.4 37.0 - - + -
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Residues in contact with PRO 208 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205J TYR* 4.5 19.3 - - + -
206J ARG* 3.8 1.5 - - - -
207J PHE* 1.3 88.5 - - - +
209J ARG* 1.3 61.0 + - - +
210J ARG 3.5 2.5 + - - +
211J VAL* 5.4 3.9 - - + +
347J VAL* 3.6 12.6 - - - +
353J VAL* 3.8 26.2 - - + -
387J LEU* 3.7 32.5 - - + -
388J HIS 3.7 10.8 - - - +
390J PRO* 3.7 11.4 - - + -
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Residues in contact with ARG 209 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171J LEU 5.5 1.0 + - - -
172J PRO 5.0 1.0 + - - -
173J ALA* 3.4 37.8 - - - +
174J GLY* 4.2 7.8 - - - +
207J PHE 3.9 6.1 - - - +
208J PRO* 1.3 75.5 - - - +
210J ARG* 1.3 63.1 + - - +
211J VAL* 5.8 0.2 - - - -
345J TYR 4.2 0.9 - - - +
346J LYS* 5.1 0.2 - - - -
347J VAL* 3.1 49.5 + - + +
388J HIS 3.3 0.2 + - - -
389J GLU* 2.5 33.9 + - + +
390J PRO 4.7 1.7 + - - -
391J ALA* 3.3 37.3 + - + +
112L GLU* 3.9 18.6 + - - +
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Residues in contact with ARG 210 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176J ASP* 4.3 7.3 + - - +
208J PRO* 3.5 1.7 - - - +
209J ARG* 1.3 82.6 - - - +
211J VAL* 1.3 68.2 + - - +
212J ARG* 4.0 28.2 - - - +
344J ASP* 2.7 30.4 + - + +
345J TYR 4.0 11.7 - - - +
346J LYS* 6.0 0.4 - - - -
387J LEU* 3.8 2.6 - - - +
388J HIS* 2.9 73.1 + - - +
389J GLU* 3.3 42.9 + - + +
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Residues in contact with VAL 211 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208J PRO 5.4 4.9 - - - +
210J ARG* 1.3 79.7 - - - +
212J ARG* 1.3 60.6 + - - +
213J VAL* 3.6 17.6 + - + -
344J ASP* 3.7 2.9 - - - -
345J TYR* 3.2 43.4 + - + +
353J VAL* 4.7 3.4 - - + -
367J ILE* 4.3 12.3 - - + -
368J VAL* 4.2 20.2 - - + -
377J VAL* 6.0 0.2 - - + -
385J VAL* 3.6 28.7 - - + -
386J HIS 3.7 2.7 - - - +
387J LEU* 3.9 17.9 - - + -
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Residues in contact with ARG 212 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210J ARG* 4.0 23.6 - - - +
211J VAL* 1.3 70.2 - - - +
213J VAL* 1.3 61.4 + - - +
214J ASP* 4.1 12.1 + - - +
342J PRO* 4.3 25.9 - - + +
343J LYS 4.7 2.7 - - - +
344J ASP* 3.3 22.4 + - - +
384J VAL 3.6 3.1 - - - +
386J HIS* 2.9 55.9 + - + +
388J HIS* 4.7 5.6 + - + -
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Residues in contact with VAL 213 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211J VAL* 3.6 24.0 - - + -
212J ARG* 1.3 74.8 - - - +
214J ASP* 1.3 68.6 + - - +
215J TYR* 3.8 26.0 - - + +
341J GLU 3.8 0.9 - - - +
343J LYS* 2.9 39.6 + - - +
345J TYR* 3.7 23.3 - - + -
361J VAL* 4.8 9.2 - - + -
367J ILE* 4.8 7.4 - - + -
379J ALA* 5.1 5.2 - - + -
384J VAL 3.4 8.7 - - - +
385J VAL* 3.9 17.5 - - + -
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Residues in contact with ASP 214 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212J ARG* 4.3 11.8 + - - +
213J VAL* 1.3 79.1 - - - +
215J TYR* 1.3 68.9 + - - +
340J THR* 5.2 5.6 - - - -
341J GLU 3.4 7.9 - - - +
342J PRO* 3.3 26.1 - - - +
382J GLU 3.4 0.5 - - - +
383J GLY* 3.2 24.4 - - - -
384J VAL* 2.9 37.7 + - + +
386J HIS* 4.2 11.2 + - - -
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Residues in contact with TYR 215 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213J VAL* 3.8 23.1 - - + +
214J ASP* 1.3 78.0 - - - +
216J LEU* 1.3 58.4 + - - +
340J THR* 2.7 30.2 + - - -
341J GLU* 2.9 36.8 + - + +
343J LYS* 3.5 25.4 - - + -
345J TYR* 2.7 35.7 + - - -
379J ALA* 4.2 2.1 - - - -
380J GLU* 3.3 48.0 + - + +
381J ALA* 3.3 35.2 - - + -
382J GLU 3.3 2.2 - - - +
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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