Contacts of the helix formed by residues 377 - 382 (chain D) in PDB entry 1M54
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 377 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111D PHE* 3.1 33.1 + - - +
116D GLY* 3.9 2.7 + - - -
345D LEU* 4.4 3.6 - - - -
346D CYS* 3.4 15.5 - - - -
376D ASP* 1.3 75.8 - - - +
378D VAL* 1.3 69.1 + - - +
379D ARG* 3.5 26.7 + - - +
380D ASN* 3.7 4.5 + - - +
381D TYR* 3.4 20.8 - - - -
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Residues in contact with VAL 378 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180C VAL* 5.8 1.3 - - + -
379C ARG* 3.9 24.9 - - - +
339D ILE* 3.7 19.7 - - + -
345D LEU* 1.9 63.4 + - + +
346D CYS 2.9 6.7 - - - +
377D SER* 1.3 75.8 - - - +
379D ARG* 1.3 64.5 + - - +
380D ASN 3.0 3.4 - - - -
381D TYR* 2.4 39.9 + - - -
382D MET* 3.4 12.1 + - + -
385D PHE* 4.9 2.9 - - + -
386D LEU* 4.4 13.2 - - + -
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Residues in contact with ARG 379 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345C LEU* 4.6 10.1 - - - +
378C VAL* 4.9 10.3 - - + -
379C ARG* 4.2 22.4 - - + -
382C MET* 4.4 26.1 - - + +
115D GLY 3.1 27.9 + - - -
116D GLY* 3.6 20.0 + - - -
117D SER 4.5 0.4 - - - +
149D ASN* 5.0 7.1 + - - -
152D ILE* 4.3 20.8 - - - +
176D GLU* 4.5 4.2 - - - +
180D VAL* 4.5 17.5 - - - +
376D ASP* 5.1 1.6 - - - +
377D SER* 3.4 21.8 + - - +
378D VAL* 1.3 82.3 - - + +
380D ASN* 1.3 78.2 + - - +
382D MET* 3.6 25.2 + - - +
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Residues in contact with ASN 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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149D ASN* 3.3 27.3 + - - +
152D ILE* 3.8 15.6 - - - +
174D SER* 4.2 10.0 + - - -
176D GLU* 4.2 16.1 - - - +
177D LYS* 3.0 50.8 + - - +
180D VAL* 4.9 1.3 - - - +
376D ASP* 3.9 9.2 + - - +
377D SER 3.7 3.4 + - - +
378D VAL 2.7 5.5 + - - -
379D ARG* 1.3 91.8 - - - +
381D TYR* 1.3 78.6 - - + +
382D MET 3.6 1.0 + - - -
384D LYS* 5.2 2.1 - - - +
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Residues in contact with TYR 381 (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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177D LYS* 6.0 0.2 - - - -
302D GLU 5.6 0.4 - - - -
304D GLU* 3.8 57.5 + - + +
332D PHE* 5.4 4.9 - + - -
347D GLY* 4.2 5.2 - - - -
348D GLY* 4.1 14.7 + - - -
349D SER 4.7 0.7 + - - -
376D ASP* 3.0 39.8 + - - -
377D SER 3.4 15.0 - - - -
378D VAL* 2.4 18.8 + - - +
380D ASN* 1.3 81.7 - - + +
382D MET* 1.3 64.8 + - - +
383D THR 3.5 2.2 - - - -
384D LYS* 2.9 30.4 + - + +
385D PHE* 3.8 36.3 - + + -
386D LEU* 3.4 12.0 - - + +
1410D PLP 3.8 3.8 - - - +
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Residues in contact with MET 382 (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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176C GLU* 3.5 26.2 - - - +
179C ASP* 5.1 4.3 - - + +
180C VAL* 3.6 32.1 - - + -
379C ARG* 3.7 27.6 - - - +
382C MET* 4.1 15.7 - - + -
176D GLU* 3.9 19.5 - - + +
378D VAL* 3.4 10.2 + - + +
379D ARG* 3.9 16.4 - - - +
380D ASN 3.5 3.4 + - - -
381D TYR* 1.3 76.7 - - - +
383D THR* 1.3 62.6 + - + +
384D LYS 3.4 1.6 + - - -
386D LEU* 3.4 41.2 - - + +
387D SER* 4.1 4.3 + - - -
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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