Contacts of the helix formed by residues 36 - 51 (chain D) in PDB entry 4Q96
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 HIS 36 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4D PHE* 3.5 46.1 - + + +
33D HIS* 3.0 13.6 + - + +
34D ARG 3.0 1.0 - - - -
35D LYS* 1.3 91.7 - - + +
37D ALA* 1.3 62.0 + - - +
38D GLY 3.3 3.0 + - - -
39D PRO* 3.4 14.4 - - + +
40D ILE* 3.0 25.1 + - + +
209D SO4 2.6 45.5 + - - -
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Residues in contact with ALA 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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34D ARG 3.1 16.5 + - - +
35D LYS 3.3 2.8 + - - +
36D HIS* 1.3 73.6 - - - +
38D GLY* 1.3 68.8 + - - +
40D ILE* 3.3 1.0 + - - +
41D VAL* 3.1 26.9 + - - +
76D GLU* 4.5 11.9 - - + -
77D PHE* 3.6 35.2 - - + -
80D GLU* 3.9 15.5 - - + -
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Residues in contact with GLY 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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35D LYS 5.2 0.4 + - - -
37D ALA* 1.3 81.0 - - - +
39D PRO* 1.3 71.1 - - - +
41D VAL* 3.2 3.5 + - - +
42D SER* 3.1 19.4 + - - -
80D GLU* 3.6 24.8 - - - +
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Residues in contact with PRO 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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4D PHE* 4.5 12.6 - - + -
6D GLU* 3.6 24.5 - - - +
35D LYS 5.5 0.2 - - - +
36D HIS* 3.4 20.9 - - + +
38D GLY* 1.3 87.1 - - - +
40D ILE* 1.3 61.8 + - - +
42D SER* 3.2 7.4 + - - -
43D VAL* 2.9 29.4 + - - +
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Residues in contact with ILE 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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4D PHE* 3.7 24.0 - - + -
9D LEU* 3.9 18.4 - - + +
30D LEU* 4.0 33.2 - - + +
33D HIS* 3.3 27.4 - - + +
36D HIS 3.0 20.4 + - - +
37D ALA 3.7 4.5 - - - +
38D GLY 3.2 0.2 - - - -
39D PRO* 1.3 76.1 - - - +
41D VAL* 1.3 56.4 + - + +
43D VAL* 3.4 1.4 + - - +
44D TRP* 2.7 38.0 + - + +
77D PHE* 3.6 31.6 - - + -
81D PHE* 5.3 4.0 - - + -
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Residues in contact with VAL 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 ALA 3.1 17.0 + - - +
38D GLY 3.8 3.6 - - - +
40D ILE* 1.3 76.3 - - - +
42D SER* 1.3 58.2 + - - +
44D TRP* 3.8 6.6 - - + +
45D HIS* 2.9 28.2 + - - +
77D PHE* 4.3 5.8 - - + -
80D GLU* 3.7 27.4 - - + +
81D PHE* 3.7 39.7 - - + -
84D VAL* 3.4 36.1 - - + -
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Residues in contact with SER 42 (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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38D GLY 3.1 13.4 + - - -
39D PRO* 3.6 11.0 - - - -
41D VAL* 1.3 78.5 - - - +
43D VAL* 1.3 56.8 - - - +
45D HIS* 3.4 4.5 + - - +
46D ARG* 2.8 54.3 + - - +
84D VAL* 6.1 1.8 - - - -
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Residues in contact with VAL 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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4D PHE* 6.0 0.2 - - + -
6D GLU* 3.6 31.0 - - + +
9D LEU* 3.8 28.3 - - + -
10D GLU* 3.8 29.2 - - + +
13D LEU* 4.0 5.6 - - + -
39D PRO 2.9 20.0 + - - +
42D SER* 1.3 72.5 - - - +
44D TRP* 1.3 65.9 + - - +
46D ARG* 3.2 29.2 + - - +
47D GLU* 3.0 25.7 + - + +
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Residues in contact with TRP 44 (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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9D LEU* 5.5 0.7 - - + -
13D LEU* 4.1 14.3 - - + +
30D LEU* 6.1 1.3 - - + -
40D ILE* 2.7 27.7 + - + +
41D VAL* 3.8 9.6 - - - +
43D VAL* 1.3 72.7 - - - +
45D HIS* 1.3 85.1 + - + +
47D GLU 3.5 0.5 + - - -
48D LEU* 2.9 44.3 + - + +
59D PHE* 2.9 59.2 + + + +
60D LEU* 4.1 11.0 - - + -
62D LEU* 4.0 20.4 - - + +
63D ALA* 3.6 18.5 - - + +
81D PHE* 3.7 30.7 - + + -
84D VAL* 4.3 9.9 - - + -
85D LEU* 4.3 4.5 - - + -
88D ALA* 4.0 22.0 - - + -
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Residues in contact with HIS 45 (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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41D VAL 2.9 18.8 + - - +
42D SER* 3.7 5.6 - - - +
44D TRP* 1.3 83.7 - + + +
46D ARG* 1.3 64.8 + - - +
48D LEU* 3.4 18.5 + - + +
49D ARG* 3.3 41.0 + - + +
84D VAL* 3.6 34.6 - - + +
87D ASP* 3.9 24.7 + - + +
88D ALA* 4.1 19.1 + - + -
91D HIS* 5.9 0.2 - - - +
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Residues in contact with ARG 46 (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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6D GLU* 3.8 10.5 + - - -
10D GLU* 5.0 7.9 + - - -
42D SER* 2.8 36.9 + - - +
43D VAL* 3.2 39.4 - - - +
45D HIS* 1.3 78.2 - - - +
47D GLU* 1.3 70.0 + - - +
49D ARG* 3.5 7.8 + - - +
50D LYS* 3.3 32.2 + - + +
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Residues in contact with GLU 47 (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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10D GLU* 4.0 25.4 - - + +
13D LEU* 3.7 20.6 - - + +
43D VAL* 3.0 26.9 + - + +
46D ARG* 1.3 81.7 + - - +
48D LEU* 1.3 61.4 + - - +
50D LYS* 3.1 31.3 + - - +
51D ALA* 2.8 15.6 + - - +
59D PHE* 3.7 18.2 - - + -
205D UNX 2.8 40.8 + - - +
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Residues in contact with LEU 48 (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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44D TRP* 2.9 33.1 + - + +
45D HIS* 3.6 12.1 - - + +
47D GLU* 1.3 75.9 - - - +
49D ARG* 1.3 52.2 + - - +
51D ALA* 3.2 9.3 + - - +
56D LYS* 2.8 56.5 + - + +
59D PHE* 3.6 33.7 - - + -
60D LEU* 4.9 1.8 - - + -
88D ALA* 3.9 33.7 - - + +
91D HIS* 4.4 9.0 - - + -
92D VAL* 3.8 15.3 - - + -
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Residues in contact with ARG 49 (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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45D HIS* 3.3 34.9 + - + +
46D ARG* 3.8 9.4 - - - +
47D GLU 3.2 0.6 - - - -
48D LEU* 1.3 76.9 - - + +
50D LYS* 1.3 60.6 + - + +
51D ALA 4.1 0.5 - - - +
56D LYS* 3.1 12.5 + - - -
87D ASP* 5.0 4.8 + - - +
91D HIS* 3.6 47.5 + - + +
95D GLU* 5.4 0.2 - - - +
202D UNX 3.3 34.3 + - - +
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Residues in contact with LYS 50 (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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10D GLU* 5.7 2.4 + - - -
46D ARG* 3.3 23.9 + - + +
47D GLU* 3.1 34.3 + - - +
49D ARG* 1.3 77.4 - - + +
51D ALA* 1.3 64.7 + - - +
52D LYS 3.8 1.2 + - - -
205D UNX 3.8 8.5 + - - +
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Residues in contact with ALA 51 (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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47D GLU 2.8 15.6 + - - +
48D LEU 3.2 9.7 + - - +
49D ARG 4.1 0.5 - - - +
50D LYS* 1.3 81.0 - - - +
52D LYS* 1.3 66.8 + - - +
53D SER 3.7 0.2 + - - -
55D ARG* 3.9 11.4 - - + +
56D LYS* 2.9 25.3 + - + -
59D PHE* 3.7 27.8 - - + -
205D UNX 3.6 7.0 - - - +
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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