Contacts of the helix formed by residues 29 - 43 (chain D) in PDB entry 1EN6
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 29 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179C ASN* 3.7 35.0 - - + +
180C ARG* 6.3 0.7 - - - +
25D ILE* 2.9 38.9 + - + +
28D THR* 1.3 97.1 - - - +
30D HIS* 1.3 65.9 + - - +
31D HIS 3.6 0.2 - - - -
32D GLN* 3.6 2.2 + - - +
33D THR* 3.1 29.1 + - - -
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Residues in contact with HIS 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170C GLU* 3.9 9.9 - - - -
174C TYR* 2.7 32.4 + + - -
179C ASN* 3.5 26.6 - - + +
25D ILE* 3.2 8.8 + - + -
26D HIS* 3.3 31.9 - - + +
29D LYS* 1.3 76.8 - - - +
31D HIS* 1.3 67.4 + - - +
33D THR* 3.1 15.6 + - - -
34D TYR* 3.2 34.5 + - + +
171D HIS* 3.6 32.7 + + + +
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Residues in contact with HIS 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D LEU* 3.5 12.4 - - + +
5D PRO* 3.8 16.8 - - + -
26D HIS 3.0 15.8 + - - +
27D HIS* 3.3 16.7 + - - +
30D HIS* 1.3 72.8 - - - +
32D GLN* 1.3 63.6 + - - +
34D TYR* 3.1 11.6 + + - +
35D VAL* 3.1 17.6 + - + +
78D HIS* 3.0 38.4 + - - -
81D HIS* 3.6 12.4 - - + +
82D SER* 3.5 25.8 - - - -
85D TRP* 2.8 32.1 + - + -
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Residues in contact with GLN 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D LEU* 3.5 28.7 - - + +
27D HIS 3.3 5.8 + - - +
28D THR* 3.2 28.9 - - - +
29D LYS* 3.8 2.2 - - - +
30D HIS 3.2 0.4 - - - -
31D HIS* 1.3 78.2 - - - +
33D THR* 1.3 58.2 + - - +
35D VAL* 3.3 12.5 + - - +
36D ASN* 2.9 62.6 + - - +
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Residues in contact with THR 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179C ASN* 5.6 2.1 + - - -
29D LYS 3.1 16.0 + - - -
30D HIS* 3.1 11.4 + - - +
32D GLN* 1.3 78.6 - - - +
34D TYR* 1.3 67.3 + - + +
36D ASN* 3.3 9.1 + - - +
37D ASN* 2.9 47.0 + - - +
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Residues in contact with TYR 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C PHE* 4.4 11.2 - + - -
30D HIS* 3.2 33.2 + - + -
31D HIS* 3.1 12.9 + + - +
33D THR* 1.3 84.6 - - + +
35D VAL* 1.3 58.1 + - - +
38D ALA* 2.9 31.9 + - - +
74D ASN* 3.6 39.4 - - - +
77D GLY* 4.1 8.7 - - - -
78D HIS* 4.1 7.0 - - - +
81D HIS* 3.4 34.8 - + - -
146D LEU* 3.6 25.1 - - + +
169D TRP* 4.4 8.5 - - - -
171D HIS* 3.8 22.3 - - - -
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Residues in contact with VAL 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D TYR* 3.4 18.6 - - + +
4D LEU* 4.1 19.7 - - + +
31D HIS* 3.1 18.9 + - + +
32D GLN* 3.6 17.9 - - - +
34D TYR* 1.3 77.3 - - - +
36D ASN* 1.3 64.2 + - - +
38D ALA* 3.8 5.0 - - - +
39D ASN* 3.0 42.4 + - - +
78D HIS* 3.6 37.5 - - + +
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Residues in contact with ASN 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D GLN* 2.9 49.1 + - - +
33D THR* 3.6 8.4 + - - +
34D TYR 3.3 0.2 - - - -
35D VAL* 1.3 80.1 - - - +
37D ASN* 1.3 60.0 + - - +
39D ASN* 3.4 6.9 + - - +
40D ALA* 3.0 28.8 + - - +
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Residues in contact with ASN 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D THR* 2.9 34.1 + - - +
36D ASN* 1.3 77.6 - - - +
38D ALA* 1.3 66.6 + - - +
40D ALA* 3.4 6.4 + - - +
41D ALA* 3.2 22.7 + - - +
70D VAL* 4.4 6.3 - - + +
74D ASN* 3.4 35.3 + - - +
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Residues in contact with ALA 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D TYR* 3.8 29.6 - - + -
34D TYR 2.9 19.6 + - - +
35D VAL* 3.8 1.6 - - - +
37D ASN* 1.3 75.2 - - - +
39D ASN* 1.3 63.9 + - - +
41D ALA* 3.2 4.0 + - - +
42D LEU* 3.0 28.8 + - - +
70D VAL 5.6 0.2 - - - -
71D LEU* 3.9 15.6 - - + +
74D ASN* 3.9 19.6 - - + +
75D ALA 4.3 0.2 - - - +
78D HIS* 5.6 0.7 - - + -
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Residues in contact with ASN 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D SER* 3.3 18.1 - - - -
2D TYR* 2.7 53.7 + - - +
35D VAL* 3.0 28.1 + - - +
36D ASN* 3.8 7.3 + - - +
38D ALA* 1.3 78.0 - - - +
40D ALA* 1.3 61.3 + - - +
42D LEU* 3.2 7.5 + - - +
43D GLU* 3.1 22.2 + - - +
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Residues in contact with ALA 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D ASN 3.0 17.4 + - - +
37D ASN* 3.7 8.7 - - - +
38D ALA 3.3 0.2 - - - -
39D ASN* 1.3 77.7 - - - +
41D ALA* 1.3 60.7 + - - +
43D GLU* 3.5 20.0 - - - +
44D SER 4.9 0.2 + - - -
67D LYS* 5.4 0.5 - - - -
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Residues in contact with ALA 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D ASN 3.2 9.2 + - - +
38D ALA 3.2 7.9 + - - +
40D ALA* 1.3 79.6 - - - +
42D LEU* 1.3 61.7 + - - +
43D GLU 3.5 0.7 + - - -
44D SER* 3.7 2.4 + - - -
45D LEU* 3.7 9.7 - - - +
67D LYS* 3.3 33.4 - - + +
70D VAL* 3.9 30.3 - - + -
71D LEU* 4.1 13.5 - - + -
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Residues in contact with LEU 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1D SER* 5.4 3.4 - - - -
2D TYR* 3.6 41.7 - - + +
38D ALA 3.0 19.4 + - - +
39D ASN* 3.2 9.8 + - - +
41D ALA* 1.3 72.9 - - - +
43D GLU* 1.3 66.5 + - - +
44D SER 3.0 3.4 - - - -
45D LEU* 2.8 33.5 + - + +
46D PRO* 5.0 0.2 - - - +
48D PHE* 4.3 2.9 - - + -
49D ALA* 3.9 40.2 - - + +
56D LEU* 4.3 9.6 - - + -
71D LEU* 3.8 27.1 - - + -
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Residues in contact with GLU 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D ASN 3.1 11.0 + - - +
40D ALA* 3.5 17.7 - - - +
41D ALA 3.3 1.0 - - - -
42D LEU* 1.3 77.5 - - - +
44D SER* 1.3 57.9 + - - +
45D LEU 3.6 0.5 + - - -
46D PRO* 4.6 7.8 - - - +
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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