Contacts of the helix formed by residues 330 - 335 (chain N) in PDB entry 2GLJ
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 ARG 330 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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310N PHE* 6.1 4.5 - - - -
328N LYS* 2.6 47.4 + - + +
329N LEU* 1.3 72.9 - - - +
331N LYS* 1.3 58.1 + - + +
332N ALA* 2.6 20.3 + - - +
333N LEU* 3.0 17.8 + - - +
334N TYR 3.7 4.3 + - - -
310P PHE* 3.2 35.9 + - - -
311P GLU* 3.0 65.8 - - + +
314P VAL* 3.5 31.2 - - + +
315P ALA* 6.2 1.6 - - + +
328P LYS* 3.1 26.4 - - - +
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Residues in contact with LYS 331 (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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96N TYR* 4.3 16.2 - - + +
329N LEU* 2.7 33.1 + - + +
330N ARG* 1.3 73.8 - - + +
332N ALA* 1.3 63.9 + - - +
333N LEU 3.2 0.2 - - - -
334N TYR* 3.7 14.8 - - + -
335N ASN* 2.9 45.8 + - - +
311P GLU* 5.1 5.6 + - - +
315P ALA* 3.3 32.5 - - - +
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Residues in contact with ALA 332 (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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95N LEU 4.2 6.3 - - - +
96N TYR* 4.1 11.7 - - - -
98N GLY* 3.6 8.1 - - - -
99N PHE* 3.3 20.6 - - + -
313N THR* 5.6 0.4 - - + -
317N ILE* 3.9 24.9 - - + -
328N LYS 5.6 0.2 - - - +
329N LEU* 3.0 23.2 - - + +
330N ARG* 2.6 7.0 + - - +
331N LYS* 1.3 72.6 - - - +
333N LEU* 1.3 61.8 + - + +
335N ASN 3.9 0.2 + - - -
336N SER* 2.9 17.0 + - - -
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Residues in contact with LEU 333 (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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99N PHE* 4.8 5.6 - - + -
101N ILE* 5.4 2.5 - - + -
309N PHE* 3.7 32.3 - - + -
310N PHE* 4.0 18.8 - - + +
313N THR* 4.4 21.1 - - + +
314N VAL* 6.4 1.3 - - + -
330N ARG* 3.0 8.7 + - - +
332N ALA* 1.3 76.5 - - + +
334N TYR* 1.3 67.9 + - - +
335N ASN 3.1 2.0 - - - -
336N SER* 2.9 23.6 + - - +
426N TYR* 3.7 48.0 - - + -
428N MET* 3.5 14.4 - - + +
311P GLU* 5.5 0.9 - - - +
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Residues in contact with TYR 334 (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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330N ARG 3.7 2.0 + - - -
331N LYS* 3.1 20.1 + - + +
333N LEU* 1.3 78.3 - - - +
335N ASN* 1.3 74.9 + - - +
336N SER 3.5 3.5 + - - +
426N TYR 3.4 18.5 + - - -
427N GLY* 3.6 35.5 - - - +
428N MET* 4.2 1.4 + - - -
429N GLN* 6.1 0.3 - - - +
79P ASN 4.5 9.5 + - - -
80P ASN* 3.4 27.0 + - - -
81P ARG* 4.6 3.5 + - - +
308P LYS* 4.9 14.4 + - + -
311P GLU* 3.2 32.0 + - - +
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Residues in contact with ASN 335 (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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96N TYR* 4.3 4.2 + - - -
97N THR 3.0 23.5 + - - +
98N GLY* 3.5 11.4 - - - -
99N PHE 4.1 0.5 + - - +
285N LYS* 5.3 2.9 - - - +
331N LYS* 2.9 45.0 + - - +
333N LEU 3.0 0.2 + - - -
334N TYR* 1.3 91.4 - - - +
336N SER* 1.3 61.6 + - - +
337N GLU* 4.9 3.9 - - - +
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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