Contacts of the helix formed by residues 373 - 380 (chain D) in PDB entry 4C3P
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 MET 373 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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308D GLU* 4.3 14.6 - - - +
309D LYS* 4.3 13.0 - - - +
312D LEU* 4.0 4.5 - - - -
372D PRO* 1.3 77.5 - - - +
374D LEU* 1.3 57.4 + - - +
375D ARG* 3.1 41.1 - - + +
376D GLU* 3.0 41.6 + - - +
377D VAL* 3.3 9.9 + - - +
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Residues in contact with LEU 374 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241D ALA* 4.0 8.6 - - + +
244D LEU* 3.7 31.9 - - + +
245D SER* 3.4 45.8 - - - +
248D HIS* 4.1 16.6 - - + +
308D GLU* 4.3 7.9 + - - +
312D LEU* 4.2 24.3 - - + +
315D LEU* 4.2 17.9 - - + -
373D MET* 1.3 69.1 - - - +
375D ARG* 1.3 62.1 + - - +
377D VAL* 3.8 9.7 - - + +
378D LEU* 3.0 33.1 + - + +
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Residues in contact with ARG 375 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373D MET* 3.1 34.3 + - + +
374D LEU* 1.3 74.2 - - - +
376D GLU* 1.3 70.1 + - - +
377D VAL 3.1 1.6 - - - -
378D LEU* 3.1 9.1 + - + +
379D GLU* 2.9 66.7 + - + +
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Residues in contact with GLU 376 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372D PRO* 3.5 21.3 - - + +
373D MET* 3.0 45.7 + - + +
375D ARG* 1.3 87.2 - - - +
377D VAL* 1.3 57.8 + - - +
379D GLU* 3.8 13.0 + - - +
380D HIS* 3.1 28.4 + - - +
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Residues in contact with VAL 377 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237D ILE* 4.1 26.0 - - + -
241D ALA* 4.4 7.6 - - + -
312D LEU* 4.4 3.6 - - + -
315D LEU* 4.3 13.9 - - + -
359D LEU* 4.6 16.2 - - + -
363D LEU* 4.1 27.1 - - + -
372D PRO* 4.3 8.3 - - + -
373D MET 3.3 11.2 + - - +
374D LEU* 3.8 13.7 - - + +
375D ARG 3.1 0.8 - - - -
376D GLU* 1.3 76.1 - - - +
378D LEU* 1.3 66.0 + - + +
379D GLU 3.2 0.2 - - - -
380D HIS* 3.3 9.7 + - - +
383D ILE* 3.2 23.3 - - + +
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Residues in contact with LEU 378 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238D THR* 3.7 30.7 - - + +
241D ALA* 3.7 25.6 - - + -
242D ASN* 3.4 28.0 - - - +
245D SER* 4.3 12.6 - - - +
374D LEU 3.0 21.0 + - - +
375D ARG* 3.1 8.8 + - + +
377D VAL* 1.3 78.7 - - + +
379D GLU* 1.3 62.3 + - + +
383D ILE* 4.3 9.3 - - + +
384D THR* 3.6 15.9 - - - +
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Residues in contact with GLU 379 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375D ARG* 2.9 58.5 + - + +
376D GLU* 3.8 10.0 - - - +
378D LEU* 1.3 79.1 - - + +
380D HIS* 1.3 66.3 + - - +
381D PRO* 3.3 4.9 - - - +
384D THR* 3.8 12.2 + - - +
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Residues in contact with HIS 380 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355D GLY* 3.4 26.0 - - - -
358D ASP* 2.7 29.6 + - + -
359D LEU* 3.9 25.6 + - + +
362D ARG* 5.0 6.7 - - - -
376D GLU 3.1 18.7 + - - +
377D VAL* 3.3 14.8 + - - +
379D GLU* 1.3 75.0 - - - +
381D PRO* 1.3 84.4 - - + +
382D TRP* 3.2 22.0 + - + +
383D ILE* 2.9 24.6 + - + +
384D THR 3.4 3.1 + - - -
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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