Contacts of the helix formed by residues 375 - 379 (chain D) in PDB entry 6NFJ
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 375 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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302D SER 5.3 0.2 + - - -
373D SER* 4.1 4.9 + - - -
374D PHE* 1.3 76.6 - - - +
376D PRO* 1.3 68.5 - - - +
377D ASN* 3.1 10.4 + - - -
378D ASN* 3.5 7.8 + - - +
379D PHE* 3.2 24.4 - - - -
416D GLU* 4.3 11.4 + - - -
418D GLY 3.7 8.3 - - - -
419D TRP* 4.4 5.6 - - - -
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Residues in contact with PRO 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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375D GLY* 1.3 81.9 - - - +
377D ASN* 1.3 66.5 + - - +
378D ASN 3.4 0.7 - - - -
379D PHE* 3.9 2.7 - - + -
380D LYS* 3.0 32.3 + - + +
416D GLU* 4.8 5.6 - - + +
418D GLY 3.2 18.6 - - - +
419D TRP* 4.1 26.7 - - + +
420D PHE* 3.7 37.5 - - + -
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Residues in contact with ASN 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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195D HIS* 6.3 1.0 - - - -
196D TRP* 4.9 11.6 - - - -
240D HIS* 6.2 0.6 - - - -
241D ASN* 4.9 1.6 - - - +
244D LEU* 3.6 29.8 - - + +
248D HIS* 4.8 1.4 + - - -
255D HIS* 5.8 1.8 - - + -
373D SER* 5.9 0.4 - - - +
375D GLY 3.1 1.8 - - - -
376D PRO* 1.3 86.7 - - - +
378D ASN* 1.3 60.8 + - - +
379D PHE 3.4 1.1 + - - -
380D LYS 3.8 9.0 - - - +
384D THR* 3.6 15.2 + - - +
416D GLU* 3.0 29.4 + - - +
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Residues in contact with ASN 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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241D ASN* 2.6 31.4 + - - +
243D TYR* 3.6 31.9 - - - -
244D LEU* 3.9 2.7 - - - +
301D GLY* 4.0 14.8 + - - -
302D SER* 4.0 28.5 + - - +
303D HIS* 3.3 23.5 + - + +
326D VAL* 4.2 4.2 - - - +
373D SER* 4.7 4.5 + - - -
374D PHE* 6.3 0.2 - - - -
375D GLY 3.5 9.3 + - - +
376D PRO 3.4 0.2 - - - -
377D ASN* 1.3 78.7 - - - +
379D PHE* 1.3 60.3 + - + +
384D THR* 3.8 11.6 - - - +
385D MET* 3.3 6.9 - - - +
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Residues in contact with PHE 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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302D SER 4.4 5.2 - - - -
303D HIS* 3.5 21.5 - - + -
304D TRP 3.4 17.0 - - - -
374D PHE* 4.3 13.0 - + - -
375D GLY 3.2 25.1 - - - +
376D PRO 3.6 1.5 + - - +
377D ASN 3.4 0.8 + - - -
378D ASN* 1.3 80.6 - - - +
380D LYS* 1.3 59.8 + - - +
381D PRO 2.9 16.1 - - - +
382D LEU* 4.5 2.3 - - - -
384D THR* 4.4 0.6 - - - +
385D MET* 3.6 14.4 - - + +
392D VAL* 3.5 26.9 - - + -
393D SER 3.2 27.6 - - - -
394D LEU* 3.5 25.6 - - + -
419D TRP* 3.8 23.3 - + + -
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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