Contacts of the helix formed by residues 302 - 312 (chain B) in PDB entry 3NX4
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 ASP 302 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298B ILE* 4.1 9.1 - - + +
299B THR* 3.0 28.2 + - - +
301B ALA* 1.3 83.1 - - - +
303B ALA* 1.3 65.1 + - - +
304B PRO* 3.4 1.8 - - - -
305B LYS* 3.2 32.2 + - - +
306B PHE* 3.1 37.1 + - + -
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Residues in contact with ALA 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B LEU* 3.8 17.9 - - + -
39B LEU* 3.5 22.5 - - + +
47B ILE* 4.5 1.8 - - + -
98B LEU* 5.1 0.7 - - + -
298B ILE* 3.9 13.7 - - + -
299B THR 3.6 2.4 + - - +
300B LEU* 3.1 21.2 + - + +
302B ASP* 1.3 77.9 - - - +
304B PRO* 1.3 56.8 - - + +
306B PHE 3.1 1.2 + - - -
307B ALA* 2.7 37.3 + - - +
321B VAL* 5.1 3.8 - - + -
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Residues in contact with PRO 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B LEU* 4.2 11.7 - - + -
15B ALA* 4.1 28.7 - - + +
16B SER* 5.6 0.7 - - - -
47B ILE* 3.9 19.4 - - + +
48B THR* 5.4 0.9 - - - +
300B LEU 4.1 1.8 - - - +
301B ALA* 3.4 19.3 - - - +
302B ASP 3.5 1.3 - - - -
303B ALA* 1.3 94.7 - - + +
305B LYS* 1.3 60.8 + - - +
307B ALA* 3.3 3.3 + - - +
308B ASP* 3.0 22.3 + - - +
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Residues in contact with LYS 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301B ALA 5.8 0.2 - - - +
302B ASP* 3.2 27.9 + - - +
303B ALA 3.2 0.4 - - - -
304B PRO* 1.3 80.7 - - - +
306B PHE* 1.3 85.9 + - + +
308B ASP* 3.3 10.3 + - - +
309B ALA* 3.1 19.8 + - + +
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Residues in contact with PHE 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B LEU* 4.0 6.1 - - + -
296B THR* 4.4 15.0 - - + -
298B ILE* 3.4 46.4 - - + -
302B ASP* 3.1 32.0 + - + +
303B ALA 3.1 6.9 + - - +
305B LYS* 1.3 98.5 - - + +
307B ALA* 1.3 61.3 + - - +
309B ALA* 3.1 6.7 + - + +
310B ILE* 2.8 37.9 + - + +
315B VAL* 4.7 16.4 - - + -
319B THR* 4.5 14.4 - - + -
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Residues in contact with ALA 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B LEU* 3.9 4.6 - - + +
44B ALA* 3.6 21.7 - - - +
47B ILE* 3.6 34.3 - - + -
48B THR* 4.0 5.6 - - + -
303B ALA 2.7 17.7 + - - +
304B PRO 3.3 10.3 + - - +
306B PHE* 1.3 71.6 - - - +
308B ASP* 1.3 63.0 + - - +
310B ILE* 3.3 2.5 + - - +
311B ILE* 3.1 28.4 + - - +
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Residues in contact with ASP 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B THR* 4.1 12.9 - - + +
304B PRO 3.0 12.5 + - - +
305B LYS* 3.3 12.1 - - - +
306B PHE 3.1 0.2 - - - -
307B ALA* 1.3 77.3 - - - +
309B ALA* 1.3 63.2 + - - +
311B ILE* 3.3 3.6 + - - +
312B ASN* 2.9 46.8 + - - +
314B GLN* 5.1 3.6 + - - +
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Residues in contact with ALA 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305B LYS* 3.1 12.8 + - + +
306B PHE* 3.1 14.4 + - + +
308B ASP* 1.3 78.0 + - - +
310B ILE* 1.3 58.8 + - - +
312B ASN 3.4 0.7 + - - -
313B ASN 3.1 3.5 + - - -
314B GLN* 2.7 54.5 + - + +
315B VAL* 3.6 21.3 + - + -
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Residues in contact with ILE 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B LEU* 3.8 37.7 - - + +
40B ASN 4.7 0.9 - - - +
41B TYR* 4.1 18.2 - - + +
44B ALA* 3.6 20.4 - - + -
306B PHE* 2.8 24.2 + - + +
307B ALA 3.6 4.0 - - - +
308B ASP 3.2 0.2 - - - -
309B ALA* 1.3 74.3 - - - +
311B ILE* 1.3 65.2 + - - +
313B ASN* 3.0 14.0 + - - +
315B VAL* 3.6 26.8 - - + +
319B THR* 3.9 14.1 - - - +
330B NAP 3.7 25.8 + - - +
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Residues in contact with ILE 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B TYR* 4.4 16.4 + - + +
44B ALA* 3.5 21.8 - - + +
45B LEU* 3.6 32.8 - - + +
48B THR* 3.6 22.7 - - + +
50B LYS* 4.2 27.6 - - + +
307B ALA 3.1 15.1 + - - +
308B ASP* 3.7 6.7 - - - +
310B ILE* 1.3 76.9 - - - +
312B ASN* 1.3 66.8 + - - +
313B ASN* 3.3 4.9 + - - +
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Residues in contact with ASN 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308B ASP* 2.9 40.7 + - - +
310B ILE 3.2 0.2 - - - -
311B ILE* 1.3 84.7 + - - +
313B ASN* 1.3 71.4 + - - +
314B GLN* 3.1 35.8 + - + +
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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