Contacts of the helix formed by residues 29 - 43 (chain A) in PDB entry 3NAV
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 ASN 29 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A GLY 3.0 9.1 + - - -
28A PRO* 1.3 86.6 + - - +
30A PRO* 1.3 68.1 - - + +
31A GLU* 3.5 17.4 + - - +
32A GLN* 2.9 37.4 + - - +
33A SER* 2.7 34.0 + - - -
74A ALA* 3.9 7.0 - - + -
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Residues in contact with PRO 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A GLY* 4.1 6.1 - - - +
29A ASN* 1.3 87.8 - - + +
31A GLU* 1.3 68.3 + - + +
33A SER* 3.1 3.4 + - - -
34A LEU* 2.8 30.5 + - - +
74A ALA* 4.3 13.2 - - + +
76A THR* 4.2 11.4 - - - +
80A ILE* 3.9 29.6 - - + -
84A LEU* 3.8 29.2 - - + +
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Residues in contact with GLU 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A ASN* 3.5 15.5 - - - +
30A PRO* 1.3 89.1 - - + +
32A GLN* 1.3 62.1 + - - +
34A LEU* 3.3 11.9 + - - +
35A ALA* 3.1 19.9 + - - +
84A LEU* 5.6 0.4 - - - -
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Residues in contact with GLN 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A PRO* 3.6 21.3 - - + -
29A ASN* 2.9 22.1 + - - +
31A GLU* 1.3 74.9 - - - +
33A SER* 1.3 61.4 + - - +
35A ALA* 3.1 9.5 + - - +
36A ILE* 2.8 34.6 + - + +
248A PRO* 3.3 38.6 + - + +
251A GLN* 3.0 29.0 + - - +
252A LEU* 3.5 21.7 - - - +
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Residues in contact with SER 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A VAL* 5.6 1.4 - - - +
24A THR 4.1 2.8 + - - -
25A ILE* 3.8 4.5 - - - +
26A GLY* 2.9 31.6 + - - -
27A ASP 3.6 17.5 + - - -
29A ASN 2.7 22.5 + - - -
30A PRO* 3.5 4.7 - - - -
32A GLN* 1.3 72.5 - - - +
34A LEU* 1.3 64.0 + - - +
36A ILE* 3.3 6.1 + - - +
37A MET* 2.9 40.7 + - - +
84A LEU* 4.5 1.3 - - - -
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Residues in contact with LEU 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A PRO 2.8 12.6 + - - +
31A GLU* 3.5 13.0 - - - +
32A GLN 3.2 0.2 - - - -
33A SER* 1.3 76.8 - - - +
35A ALA* 1.3 61.4 + - - +
37A MET* 3.3 9.2 + - + +
38A GLN* 3.1 23.9 + - + +
84A LEU* 4.1 16.8 - - + +
87A GLN* 3.2 42.4 - - + +
88A ILE* 3.7 30.0 - - + +
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Residues in contact with ALA 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A GLU 3.1 13.1 + - - +
32A GLN* 3.1 19.5 + - - +
34A LEU* 1.3 76.5 - - - +
36A ILE* 1.3 58.8 + - - +
38A GLN* 3.4 5.8 + - - +
39A THR* 2.8 35.6 + - - -
252A LEU* 4.0 18.6 - - + -
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Residues in contact with ILE 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A VAL* 4.1 29.4 - - + -
27A ASP 3.3 25.8 - - - +
28A PRO* 3.7 13.9 - - + -
32A GLN* 2.8 25.1 + - + +
33A SER* 3.4 6.1 - - - +
35A ALA* 1.3 75.8 - - - +
37A MET* 1.3 64.9 + - - +
39A THR* 3.0 4.2 + - - +
40A LEU* 3.0 26.3 + - + +
241A ILE* 3.7 20.6 - - + -
251A GLN* 4.1 3.4 - - - +
252A LEU* 3.8 15.2 - - + +
255A LEU* 3.8 25.7 - - + +
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Residues in contact with MET 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A VAL* 4.1 13.2 - - + -
25A ILE* 4.5 9.4 - - + -
33A SER* 2.9 41.6 + - - +
34A LEU* 3.9 8.3 - - + +
36A ILE* 1.3 75.5 - - - +
38A GLN* 1.3 61.4 + - - +
40A LEU* 3.2 8.8 + - + +
41A ILE* 3.2 25.3 + - - +
48A LEU* 4.0 11.9 - - + +
50A LEU* 3.7 44.0 - - + -
84A LEU* 4.4 21.8 - - + +
85A ILE* 5.8 0.9 - - - -
88A ILE* 3.7 30.1 - - + -
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Residues in contact with GLN 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A LEU* 3.1 17.3 + - + +
35A ALA* 3.7 7.0 - - - +
37A MET* 1.3 76.3 - - - +
39A THR* 1.3 57.8 + - - +
41A ILE* 3.3 4.5 + - - +
42A ASP* 2.6 68.8 + - - +
88A ILE* 3.9 10.6 - - + +
91A ARG* 4.0 11.0 - - - +
92A ASN* 2.8 42.0 + - - +
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Residues in contact with THR 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A ALA 2.8 22.5 + - - -
36A ILE* 3.0 7.4 + - - -
38A GLN* 1.3 75.7 - - - +
40A LEU* 1.3 60.8 + - - +
42A ASP* 3.8 8.8 - - - +
43A ALA* 2.9 28.6 + - - +
252A LEU* 3.5 47.4 - - + +
255A LEU* 4.4 7.0 - - + -
256A ALA* 4.0 18.8 - - + +
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Residues in contact with LEU 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A PRO* 3.9 25.6 - - + +
23A VAL* 3.7 33.7 - - + -
36A ILE* 3.0 23.3 + - + +
37A MET* 3.2 8.3 + - - +
39A THR* 1.3 79.4 - - - +
41A ILE* 1.3 59.0 + - - +
43A ALA* 3.4 4.3 + - - -
44A GLY 3.5 0.5 + - - -
45A ALA* 2.9 26.2 + - - +
48A LEU* 4.0 17.9 - - + -
237A VAL* 4.0 17.9 - - + -
255A LEU* 4.3 16.4 - - + +
259A THR* 3.2 29.0 - - - +
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Residues in contact with ILE 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A MET 3.2 11.8 + - - +
38A GLN* 3.6 11.2 - - - +
40A LEU* 1.3 78.1 - - - +
42A ASP* 1.3 65.5 + - - +
44A GLY* 3.2 13.7 + - - -
45A ALA* 3.9 12.3 + - - +
48A LEU* 3.8 19.7 - - + -
88A ILE* 3.8 19.7 - - + -
92A ASN* 3.4 43.5 - - + +
95A THR* 3.9 31.9 - - + +
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Residues in contact with ASP 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A GLN* 2.6 53.8 + - - +
39A THR* 3.8 7.7 - - - +
40A LEU 3.3 0.2 - - - -
41A ILE* 1.3 79.1 - - - +
43A ALA* 1.3 61.0 + - - +
44A GLY* 3.4 1.2 + - - -
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Residues in contact with ALA 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A THR 2.9 18.0 + - - +
40A LEU 3.4 0.2 + - - -
41A ILE 3.2 0.4 - - - -
42A ASP* 1.3 77.2 - - - +
44A GLY* 1.3 55.7 + - - +
45A ALA 3.9 0.9 - - - -
256A ALA* 3.7 38.8 - - + +
259A THR* 3.8 16.5 - - + +
260A GLN* 3.6 30.4 - - - +
263A LYS* 5.0 1.6 - - - +
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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