Contacts of the helix formed by residues 34 - 47 (chain B) in PDB entry 3NA1
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 LYS 34 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B THR* 3.3 35.0 - - + +
31B GLY 3.1 6.8 + - - -
33B HIS* 1.3 86.9 + - + +
35B VAL* 1.3 65.3 + - - +
36B HIS* 3.2 19.7 - - + -
37B LEU* 3.0 33.2 + - + -
38B HIS 3.1 9.5 + - - -
456B THR 3.6 9.4 + - - +
457B THR* 3.4 31.7 + - - -
465B GLU* 4.8 13.4 - - - +
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Residues in contact with VAL 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B PHE* 3.7 19.3 - - + -
31B GLY 4.0 0.4 + - - -
32B THR 3.3 20.2 - - - +
33B HIS 3.6 1.2 - - - -
34B LYS* 1.3 77.6 - - - +
36B HIS* 1.3 64.5 + - - +
38B HIS* 3.1 13.1 + - + +
39B HIS* 3.1 46.9 + - + +
209B LEU* 5.6 2.7 - - + -
210B ASN* 6.2 0.9 - - - +
353B VAL* 4.5 9.6 - - + -
458B PHE* 3.5 30.0 - - + +
602B HCD 5.9 4.5 - - + +
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Residues in contact with HIS 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B HIS 3.7 10.5 + - - -
34B LYS* 3.7 24.7 - - + +
35B VAL* 1.3 78.8 + - - +
37B LEU* 1.3 83.6 + - + +
39B HIS* 3.3 7.6 + - - +
40B VAL* 3.3 24.1 + - - +
353B VAL* 3.7 20.1 - - + +
381B TYR* 3.6 49.9 - + + -
456B THR* 3.0 41.6 + - + -
457B THR* 4.1 2.2 - - - -
458B PHE* 4.2 1.5 - - - +
462B LEU* 3.9 13.1 - - + +
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Residues in contact with LEU 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B THR* 4.6 4.7 - - + -
34B LYS* 3.0 33.4 + - + +
36B HIS* 1.3 99.3 - - + +
38B HIS* 1.3 60.9 + - - +
40B VAL* 3.3 10.0 + - + +
41B GLN* 2.9 46.9 + - + +
381B TYR* 4.4 12.1 - - + +
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Residues in contact with HIS 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B PHE* 3.5 47.7 - + + -
30B THR* 4.0 12.4 + - + +
34B LYS 3.1 11.1 + - - +
35B VAL* 3.2 11.7 - - + +
37B LEU* 1.3 77.1 - - - +
39B HIS* 1.3 67.2 + + - +
41B GLN* 3.4 11.0 + - - +
42B ASN* 2.9 60.5 + - - -
45B LYS* 6.3 0.2 - - - -
52B GLU* 2.8 34.8 + - - -
54B LEU* 5.0 5.3 - - + +
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Residues in contact with HIS 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B VAL* 3.1 35.6 + - + +
36B HIS* 3.6 7.1 - - - +
38B HIS* 1.3 86.6 - + - +
40B VAL* 1.3 62.4 + - - +
42B ASN* 3.1 2.4 + - - +
43B PHE* 3.0 31.1 + - + -
50B TYR* 3.6 22.0 - - - +
61B TYR* 3.7 19.7 + + - -
353B VAL* 4.0 15.9 + - + +
354B THR* 3.5 31.2 - - + +
377B GLN* 5.4 0.2 - - - -
379B ALA* 4.3 22.1 - - + +
381B TYR* 5.8 1.4 - - + +
382B ALA* 4.4 4.3 - - + +
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Residues in contact with VAL 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B HIS 3.3 14.9 + - - +
37B LEU* 3.3 14.8 + - + +
39B HIS* 1.3 76.9 - - - +
41B GLN* 1.3 65.1 + - + +
43B PHE* 3.3 4.6 + - - +
44B GLN* 3.2 42.5 + - + +
381B TYR* 4.1 18.6 - - + -
382B ALA* 4.0 24.5 - - + +
385B ARG* 5.5 7.0 - - + -
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Residues in contact with GLN 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B THR* 3.4 23.5 + - - +
37B LEU* 2.9 31.7 + - + +
38B HIS* 3.7 9.3 + - - +
40B VAL* 1.3 78.7 - - + +
42B ASN* 1.3 59.9 + - - +
44B GLN* 3.4 19.9 + - - +
45B LYS* 3.0 38.5 + - - +
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Residues in contact with ASN 42 (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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15B PRO* 6.0 0.2 - - - +
38B HIS* 2.9 55.1 + - - +
39B HIS 3.1 1.3 + - - +
41B GLN* 1.3 77.3 - - - +
43B PHE* 1.3 57.4 + - - +
45B LYS* 3.2 13.5 + - - -
46B TYR* 2.8 54.7 + - + +
50B TYR* 3.2 41.0 + - + +
52B GLU* 3.4 11.2 + - - +
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Residues in contact with PHE 43 (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 HIS* 3.0 30.5 + - + -
40B VAL* 3.3 5.8 + - - +
42B ASN* 1.3 73.6 - - - +
44B GLN* 1.3 64.6 + - + +
47B GLY* 3.0 41.2 + - - +
48B PRO* 3.7 17.7 - - + -
50B TYR* 3.5 28.5 - + - -
61B TYR* 4.0 7.4 - - + -
62B VAL 3.8 11.7 - - - -
63B ILE* 3.7 35.7 - - + -
379B ALA* 3.3 32.5 - - + -
382B ALA* 3.9 13.5 - - + -
386B GLU* 6.0 1.6 - - - +
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Residues in contact with GLN 44 (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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40B VAL* 3.2 32.0 + - + +
41B GLN* 3.6 23.7 - - - +
42B ASN 3.3 0.2 - - - -
43B PHE* 1.3 77.3 - - + +
45B LYS* 1.3 60.8 + - - +
47B GLY 4.6 1.2 + - - -
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Residues in contact with LYS 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B GLU* 4.9 10.1 + - - -
41B GLN* 3.0 26.0 + - - +
42B ASN* 3.4 16.2 + - - +
43B PHE 3.1 0.2 - - - -
44B GLN* 1.3 79.6 - - - +
46B TYR* 1.3 93.4 + - + +
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Residues in contact with TYR 46 (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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13B PRO* 3.8 34.1 - - + +
14B SER 4.0 14.4 - - - -
15B PRO* 3.2 43.8 - - + +
42B ASN* 2.8 48.2 + - - +
45B LYS* 1.3 101.5 + - + +
47B GLY* 1.3 60.0 + - - +
48B PRO* 4.7 0.9 - - - +
49B ILE 4.2 2.2 - - - +
50B TYR* 3.8 34.8 - + + -
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Residues in contact with GLY 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B PHE* 3.0 36.3 + - - +
44B GLN 4.6 1.2 + - - -
45B LYS 3.7 0.8 - - - -
46B TYR* 1.3 82.1 - - - +
48B PRO* 1.3 68.2 - - - +
49B ILE 3.2 11.2 + - - +
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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
------------------------------------------------------------
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