Contacts of the helix formed by residues 319 - 331 (chain C) in PDB entry 2NT0
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 319 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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286C LEU* 5.0 1.8 - - + -
317C LEU* 4.0 4.9 - - + -
318C ALA* 1.3 84.1 - - - +
320C ALA* 1.3 63.4 + - - +
321C LYS* 3.5 2.9 - - + +
322C ALA* 3.7 12.2 + - + +
323C THR* 3.0 25.3 + - - +
286D LEU* 3.9 42.2 - - + +
288D LEU 5.9 1.3 - - - +
323D THR* 6.3 0.9 - - + -
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Residues in contact with ALA 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285C ARG* 4.4 2.9 - - - +
318C ALA 3.2 6.9 + - - +
319C PRO* 1.3 71.2 - - - +
321C LYS* 1.3 62.9 + - - +
323C THR* 3.6 5.8 - - - -
324C LEU* 2.8 38.1 + - + +
325C GLY 2.9 6.0 + - - -
369C THR* 3.6 22.7 - - + -
373C TYR* 3.6 30.5 - - + -
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Residues in contact with LYS 321 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319C PRO* 3.5 2.1 - - + +
320C ALA* 1.3 78.3 - - - +
322C ALA* 1.3 57.2 + - - +
325C GLY* 3.0 7.8 + - - +
326C GLU* 2.8 28.8 + - - +
373C TYR* 3.6 33.1 - - + +
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Residues in contact with ALA 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288C LEU 4.1 0.2 - - - +
289C PRO* 3.5 14.4 - - - +
319C PRO* 3.7 15.9 + - + +
320C ALA 3.3 0.4 - - - -
321C LYS* 1.3 79.2 - - - +
323C THR* 1.3 62.4 + - + +
326C GLU* 3.4 19.8 - - - +
1594C GOL 5.0 1.2 + - - -
322D ALA* 4.6 20.4 - - + -
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Residues in contact with THR 323 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285C ARG* 3.4 49.7 - - + +
286C LEU* 4.0 24.0 - - + -
288C LEU* 3.6 19.1 - - - +
289C PRO 4.5 0.3 - - - -
319C PRO 3.0 19.8 + - - +
320C ALA* 3.3 2.9 + - - -
322C ALA* 1.3 85.3 - - + +
324C LEU* 1.3 68.2 + - - +
326C GLU* 3.7 0.5 + - - +
327C THR* 2.7 33.5 + - - -
319D PRO* 6.1 1.8 - - + -
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Residues in contact with LEU 324 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285C ARG* 4.2 20.2 - - - +
288C LEU* 4.4 4.9 - - + -
310C VAL* 4.3 21.1 - - + -
320C ALA* 2.8 19.3 + - + +
323C THR* 1.3 83.6 + - - +
325C GLY* 1.3 65.6 + - - +
327C THR* 3.4 3.9 + - - -
328C HIS* 3.1 23.4 + - - +
336C LEU* 3.8 28.7 - - + +
369C THR* 5.0 0.9 - - + +
370C ASN* 4.1 16.4 - - - +
373C TYR* 3.8 26.7 - - + +
374C HIS* 4.5 0.2 - - - -
375C VAL* 3.9 25.8 - - + -
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Residues in contact with GLY 325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320C ALA 2.9 11.1 + - - -
321C LYS* 3.0 12.8 - - - -
324C LEU* 1.3 75.0 - - - +
326C GLU* 1.3 58.1 + - - +
328C HIS* 3.2 5.5 + - - +
329C ARG* 3.0 27.6 + - - +
373C TYR* 3.9 19.1 - - - -
374C HIS* 4.6 8.7 + - - -
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Residues in contact with GLU 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289C PRO* 3.5 21.8 - - + -
321C LYS 2.8 10.7 + - - +
322C ALA* 3.4 23.1 - - - +
323C THR 3.7 0.4 + - - -
324C LEU 3.3 0.2 - - - -
325C GLY* 1.3 70.1 - - - +
327C THR* 1.3 67.2 + - - +
329C ARG* 2.7 48.1 + - - +
330C LEU* 2.9 39.1 + - + +
1594C GOL 5.9 0.7 - - - -
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Residues in contact with THR 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288C LEU* 3.3 20.3 - - + +
289C PRO* 3.3 14.7 - - - +
292C ALA* 3.9 13.9 - - + -
308C ILE* 3.7 30.3 - - + -
323C THR 2.7 23.7 + - - -
324C LEU 3.7 4.5 - - - -
326C GLU* 1.3 78.4 - - - +
328C HIS* 1.3 56.6 + - - +
330C LEU* 3.3 3.1 + - - -
331C PHE* 2.8 32.7 + - + +
334C THR 6.0 0.2 - - - +
336C LEU* 4.0 17.9 - - + -
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Residues in contact with HIS 328 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324C LEU 3.1 9.1 + - - +
325C GLY 3.6 4.9 + - - +
327C THR* 1.3 75.9 - - - +
329C ARG* 1.3 60.9 + - - +
331C PHE 4.1 5.6 - - - -
332C PRO* 2.9 61.8 + - + +
334C THR 5.5 3.6 - - - -
336C LEU* 4.3 10.2 - - + +
374C HIS* 3.4 52.1 + + + -
1591C GOL 3.0 45.2 + - - -
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Residues in contact with ARG 329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325C GLY 3.0 13.8 + - - +
326C GLU* 2.7 46.5 + - - +
328C HIS* 1.3 82.6 + - - +
330C LEU* 1.3 81.0 + - - +
332C PRO* 3.6 11.9 - - - +
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Residues in contact with LEU 330 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289C PRO* 4.0 16.6 - - + -
293C LYS* 3.8 38.6 - - + -
326C GLU* 2.9 32.8 + - + +
327C THR 3.8 0.7 - - - +
329C ARG* 1.3 104.4 - - - +
331C PHE* 1.3 83.7 + - + +
332C PRO* 3.5 5.6 - - - +
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Residues in contact with PHE 331 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289C PRO* 5.8 0.2 - - + -
292C ALA* 3.7 25.1 - - + -
293C LYS* 3.7 30.1 - - + -
296C LEU* 3.7 37.2 - - + -
297C THR* 3.8 28.5 - - + -
308C ILE* 5.3 0.4 - - + -
327C THR* 2.8 20.2 + - + +
328C HIS* 3.2 7.4 - - - +
330C LEU* 1.3 100.9 - - + +
332C PRO* 1.3 62.5 - - - +
333C ASN 3.1 7.4 + - - -
334C THR* 3.3 24.5 + - - +
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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