Contacts of the strand formed by residues 303 - 312 (chain N) in PDB entry 4G7H
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 PRO 303 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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250N LEU* 3.9 35.9 - - + -
251N PHE 3.8 6.5 - - - +
252N ARG* 3.5 24.2 - - + +
291N LEU* 4.0 19.9 - - + +
292N VAL* 4.0 12.0 - - - +
302N GLN* 1.3 92.9 + - + +
304N LEU* 1.3 61.7 + - - +
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Residues in contact with LEU 304 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251N PHE* 2.8 23.4 + - + +
253N ALA* 3.7 30.1 - - + +
259N VAL* 4.6 0.2 - - + -
270N LEU* 4.3 20.6 - - + +
272N LEU* 4.4 2.9 - - + -
282N TYR* 3.5 38.4 - - + -
284N LEU* 5.1 1.2 - - + +
290N PRO* 3.6 4.5 - - - +
291N LEU* 2.8 21.0 + - - -
292N VAL* 3.8 23.0 + - + +
298N VAL* 3.8 33.0 - - + -
302N GLN 3.2 2.0 + - - +
303N PRO* 1.3 73.0 - - - +
305N ALA* 1.3 61.1 + - + +
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Residues in contact with ALA 305 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250N LEU* 3.3 7.3 - - - +
251N PHE* 3.1 30.0 + - + -
284N LEU* 4.0 17.9 - - + -
288N MET* 3.7 24.7 - - + -
289N THR 3.3 14.6 - - - +
290N PRO* 4.3 0.9 - - + -
291N LEU* 3.6 13.9 - - - +
303N PRO* 3.5 1.8 - - - +
304N LEU* 1.3 81.9 - - - +
306N GLU* 1.3 60.8 + - - +
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Residues in contact with GLU 306 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248N PRO* 3.7 31.0 - - - +
249N TYR 3.9 2.5 - - - -
250N LEU* 4.4 16.6 - - + +
287N GLY 3.8 0.5 - - - +
288N MET* 3.5 2.5 - - - -
289N THR* 2.9 46.9 + - - +
291N LEU* 3.9 16.5 - - + +
305N ALA* 1.3 72.9 - - - +
307N ALA* 1.3 64.8 + - - +
308N LYS* 3.4 33.2 + - + +
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Residues in contact with ALA 307 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225N LEU* 5.5 0.4 - - + -
245N LEU* 3.2 24.7 - - + +
248N PRO* 3.4 2.1 - - - +
249N TYR* 2.9 48.6 + - + +
251N PHE 5.2 0.2 - - - +
287N GLY 3.7 4.9 - - - -
288N MET* 3.6 33.8 - - + +
305N ALA 4.1 0.4 - - - -
306N GLU* 1.3 71.6 - - - +
308N LYS* 1.3 61.3 - - - +
311N LEU* 4.3 4.7 - - + -
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Residues in contact with LYS 308 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245N LEU* 4.3 1.1 - - - +
248N PRO* 4.2 20.6 - - + -
287N GLY* 3.1 19.3 + - - +
289N THR* 5.9 2.9 - - - -
306N GLU* 3.4 31.8 + - + +
307N ALA* 1.3 75.8 - - - +
309N GLY* 1.3 72.2 + - - +
310N LEU 3.3 8.3 + - - +
311N LEU* 5.1 0.3 - - - +
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Residues in contact with GLY 309 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245N LEU* 2.7 53.9 + - - +
247N GLU* 5.6 0.6 - - - +
248N PRO* 5.4 2.6 - - - +
307N ALA 4.4 0.2 + - - -
308N LYS* 1.3 76.4 - - - +
310N LEU* 1.3 57.1 + - - -
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Residues in contact with LEU 310 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241N ILE* 3.6 33.0 - - + -
243N ALA 3.4 14.1 - - - +
244N GLU* 3.9 17.5 - - + +
286N VAL* 4.3 2.8 - - - +
287N GLY* 4.4 4.5 - - - -
308N LYS 3.3 5.6 + - - +
309N GLY* 1.3 74.5 - - - -
311N LEU* 1.3 61.5 + - - +
312N ARG* 4.3 10.2 + - - +
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Residues in contact with LEU 311 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225N LEU* 4.4 10.1 - - + -
241N ILE* 3.8 3.1 - - - +
242N LEU* 2.9 37.7 + - + -
243N ALA* 2.9 46.0 + - + +
245N LEU* 3.6 36.1 - - + -
285N PRO* 4.0 20.6 - - + -
286N VAL 3.1 19.7 - - - +
287N GLY* 4.1 7.0 - - - -
288N MET* 4.1 7.6 - - + -
307N ALA* 4.3 9.0 - - + -
308N LYS 5.1 1.3 - - - +
310N LEU* 1.3 75.5 - - - +
312N ARG* 1.3 59.8 + - - +
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Residues in contact with ARG 312 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239N GLY* 2.4 37.1 + - - +
240N GLU* 3.3 17.2 - - - +
241N ILE* 3.3 35.2 - - + +
242N LEU* 3.8 3.8 - - - +
266N GLU* 6.0 0.9 - - - -
285N PRO* 3.4 7.4 - - - +
286N VAL* 3.0 46.3 + - + +
310N LEU* 4.9 12.1 + - - +
311N LEU* 1.3 75.6 - - - +
313N MET* 1.3 72.4 + - - +
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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