Contacts of the helix formed by residues 16 - 31 (chain B) in PDB entry 3NTE
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 SER 16 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188A THR* 5.6 3.1 - - - -
14B ALA* 3.3 5.7 + - - -
15B ILE* 1.3 76.8 - - - +
17B PRO* 1.3 67.7 - - - +
18B ARG* 3.0 35.0 + - - +
19B THR* 2.8 31.5 + - - -
20B LEU* 3.0 9.5 + - - +
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Residues in contact with PRO 17 (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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14B ALA* 6.5 0.2 - - + -
15B ILE 3.9 4.7 - - - +
16B SER* 1.3 87.8 - - - +
18B ARG* 1.3 55.2 + - - +
20B LEU* 3.7 14.8 - - + +
21B ASN* 2.8 41.0 + - - +
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Residues in contact with ARG 18 (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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180A GLU* 4.5 3.9 - - + +
183A ASN* 3.5 29.2 + - + -
184A TRP* 3.6 14.5 - - - +
187A GLU* 2.8 56.0 + - - +
188A THR* 3.9 14.5 - - - +
16B SER* 3.0 15.3 + - - +
17B PRO* 1.3 79.1 - - - +
19B THR* 1.3 59.3 + - - +
21B ASN* 3.7 14.1 - - + +
22B ALA* 3.1 26.7 + - - +
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Residues in contact with THR 19 (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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184A TRP* 3.4 31.8 + - + +
188A THR* 4.1 9.0 + - - +
15B ILE* 3.3 28.3 - - + -
16B SER* 2.8 21.3 + - - -
18B ARG* 1.3 77.0 - - - +
20B LEU* 1.3 59.5 + - - +
22B ALA* 3.4 3.7 + - - +
23B TRP* 3.1 26.0 + - - +
43B LEU* 3.7 26.2 - - + +
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Residues in contact with LEU 20 (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 ILE* 3.6 39.3 - - + +
16B SER 3.0 10.6 + - - +
17B PRO* 3.7 13.9 - - + +
18B ARG 3.3 0.2 - - - -
19B THR* 1.3 74.8 - - - +
21B ASN* 1.3 65.1 + - - +
23B TRP* 3.1 5.5 + - + +
24B VAL* 3.0 29.0 + - - +
54B THR* 4.0 20.9 - - + -
55B MET* 4.0 29.8 - - + -
58B THR* 4.7 16.6 - - + +
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Residues in contact with ASN 21 (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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180A GLU* 4.3 15.0 - - + +
17B PRO* 2.8 35.3 + - - +
18B ARG* 3.7 14.5 - - + +
19B THR 3.4 0.2 - - - -
20B LEU* 1.3 74.4 - - - +
22B ALA* 1.3 59.0 + - - +
24B VAL* 2.9 28.5 - - - +
25B LYS* 3.2 10.2 + - - +
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Residues in contact with ALA 22 (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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180A GLU* 3.5 30.0 - - - +
181A VAL* 3.7 11.5 - - + +
184A TRP* 3.7 17.3 - - + -
18B ARG 3.1 15.6 + - - +
19B THR 3.7 5.2 - - - +
20B LEU 3.2 0.2 - - - -
21B ASN* 1.3 76.6 - - - +
23B TRP* 1.3 61.5 + - - +
25B LYS* 3.4 0.7 + - - +
26B VAL* 3.1 29.4 + - - +
43B LEU* 4.3 9.4 - - + -
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Residues in contact with TRP 23 (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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19B THR 3.1 14.6 + - - +
20B LEU* 3.1 8.7 + - + +
22B ALA* 1.3 74.0 - - - +
24B VAL* 1.3 64.1 + - - +
26B VAL* 3.3 9.0 + - + -
27B VAL* 3.2 43.7 + - + +
36B VAL* 3.9 21.5 - - + -
40B PHE* 3.6 47.8 - + + -
43B LEU* 3.9 22.1 - - + +
55B MET* 3.1 56.5 + - + +
56B LEU* 5.1 7.4 - - + -
58B THR* 3.5 17.5 - - + -
59B VAL* 3.9 15.2 - - + +
138B LEU* 5.0 8.1 - - + -
227B I3M 5.6 4.0 - - + -
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Residues in contact with VAL 24 (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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20B LEU 3.0 13.7 + - - +
21B ASN* 2.9 33.2 - - - +
23B TRP* 1.3 75.9 - - - +
25B LYS* 1.3 68.9 + - - +
27B VAL* 3.3 3.3 + - - +
28B GLU* 2.9 28.4 + - - +
58B THR* 3.1 44.9 - - + +
59B VAL* 4.2 9.6 - - + +
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Residues in contact with LYS 25 (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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178A SER* 3.0 32.3 - - - +
180A GLU* 3.4 39.1 + - + +
181A VAL* 4.5 0.9 - - + -
21B ASN 3.2 5.3 + - - +
22B ALA* 3.7 3.8 - - - +
23B TRP 3.2 0.6 - - - -
24B VAL* 1.3 89.6 - - - +
26B VAL* 1.3 59.4 + - - +
28B GLU* 2.6 32.4 + - - +
29B GLU* 2.9 53.4 + - + +
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Residues in contact with VAL 26 (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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147A PRO* 5.8 1.6 - - + -
181A VAL* 3.4 20.9 - - + -
222A IOD 4.5 12.8 - - + -
22B ALA 3.1 21.1 + - - +
23B TRP* 3.6 20.0 - - + +
25B LYS* 1.3 75.0 - - - +
27B VAL* 1.3 58.9 + - - +
30B LYS* 2.8 36.4 + - + +
36B VAL* 4.6 14.3 - - + +
39B MET* 4.0 40.6 - - + -
43B LEU* 4.4 5.6 - - + -
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Residues in contact with VAL 27 (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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23B TRP* 3.2 49.0 + - + +
24B VAL 3.6 7.4 - - - +
25B LYS 3.1 0.6 - - - -
26B VAL* 1.3 76.1 - - + +
28B GLU* 1.3 66.2 + - - +
31B ALA* 2.9 36.5 + - + +
36B VAL* 5.0 6.1 - - + -
59B VAL* 3.7 20.2 - - + -
62B HIS* 3.4 34.6 - - + +
227B I3M 4.2 11.4 - - + -
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Residues in contact with GLU 28 (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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24B VAL 2.9 16.0 + - - +
25B LYS* 2.6 37.1 + - - +
27B VAL* 1.3 79.5 - - - +
29B GLU* 1.3 79.0 + - - +
31B ALA* 4.8 1.6 + - - +
62B HIS* 5.5 3.4 - - - -
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Residues in contact with GLU 29 (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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178A SER* 5.1 2.7 - - - -
222A IOD 4.2 18.4 - - + -
25B LYS* 2.9 33.4 + - + +
26B VAL 4.1 2.0 - - - +
28B GLU* 1.3 100.8 - - - +
30B LYS* 1.3 76.7 + - + +
31B ALA 3.6 0.9 - - - -
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Residues in contact with LYS 30 (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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31A ALA* 5.0 13.9 - - - +
32A PHE* 5.8 3.8 - - - +
146A SER* 6.0 0.2 - - - +
147A PRO* 4.3 19.7 - - + +
176A GLN 4.6 10.3 + - - -
26B VAL* 2.8 28.2 + - + +
29B GLU* 1.3 90.0 + - + +
31B ALA* 1.3 70.1 + - - +
32B PHE 3.2 0.2 + - - -
33B SER* 2.8 31.7 + - - +
35B GLU* 3.6 26.5 - - + +
36B VAL* 3.3 18.2 - - + +
39B MET* 6.5 0.2 - - + -
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Residues in contact with ALA 31 (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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27B VAL* 2.9 26.3 + - + +
28B GLU 5.2 1.6 - - - +
29B GLU 3.6 1.8 - - - -
30B LYS* 1.3 78.8 - - - +
32B PHE* 1.3 96.1 + - + +
33B SER* 3.2 2.4 + - - -
36B VAL* 4.1 7.0 - - - -
62B HIS* 4.2 14.1 - - + -
227B I3M 4.8 4.7 - - + -
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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