Contacts of the helix formed by residues 38 - 58 (chain D) in PDB entry 4ZZ7
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 38 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15D GLU* 2.7 37.9 + - - -
17D THR* 4.8 3.1 - - - -
18D ARG* 5.8 0.2 - - - -
36D LEU 3.6 0.8 + - - -
37D ALA* 1.3 73.6 - - - +
39D THR* 1.3 69.5 + - - +
40D LYS* 3.8 11.7 + - - +
41D THR 2.9 12.0 + - - -
42D VAL* 3.1 14.1 + - - +
206D GLU* 3.5 23.3 - - - -
234F ARG* 5.7 8.1 - - - -
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Residues in contact with THR 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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38D SER* 1.3 74.2 - - - +
40D LYS* 1.3 64.2 + - - +
42D VAL* 3.4 1.4 + - - +
43D GLU* 3.0 42.8 + - - +
206D GLU* 3.7 25.0 + - + +
209D ASP* 6.2 0.7 - - + -
210D ALA* 3.9 28.9 - - + +
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Residues in contact with LYS 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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15D GLU* 6.0 0.4 - - - -
38D SER* 3.1 9.7 + - - +
39D THR* 1.3 83.8 + - - +
41D THR* 1.3 60.8 + - - +
43D GLU* 3.5 12.7 + - - +
44D GLN* 3.2 41.6 + - + +
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Residues in contact with THR 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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6D HIS* 3.9 17.7 - - + -
8D ILE* 3.7 21.4 - - + +
13D VAL* 5.4 1.8 - - + -
15D GLU* 2.6 38.8 + - + +
37D ALA* 3.8 17.0 - - + -
38D SER* 2.9 6.3 + - - -
40D LYS* 1.3 76.4 - - - +
42D VAL* 1.3 65.1 + - - +
44D GLN* 3.1 27.7 + - - +
45D ALA* 3.2 9.7 + - - +
201D VAL* 4.1 2.9 - - + -
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Residues in contact with VAL 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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37D ALA* 4.3 3.8 - - + -
38D SER 3.1 12.3 + - - +
39D THR 3.7 6.3 - - - +
41D THR* 1.3 75.5 - - - +
43D GLU* 1.3 58.7 + - + +
45D ALA* 2.9 5.7 + - - +
46D ILE* 2.9 44.9 + - + +
170D VAL* 5.2 0.9 - - + -
201D VAL* 3.9 20.6 - - + -
207D ALA* 3.8 35.2 - - + +
210D ALA* 3.7 19.7 - - + -
211D LEU* 3.9 19.1 - - + -
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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 THR* 3.0 35.2 + - - +
40D LYS* 3.6 10.9 - - - +
42D VAL* 1.3 78.1 - - + +
44D GLN* 1.3 52.6 + - + +
46D ILE* 3.8 4.9 - - + -
47D SER* 2.5 39.5 + - - +
210D ALA* 5.7 4.0 - - + +
214D ASP* 3.9 18.1 - - - +
216D ARG* 3.8 13.1 + - - +
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Residues in contact with GLN 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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8D ILE* 3.8 16.1 - - + +
13D VAL* 5.3 4.5 - - - +
40D LYS* 3.2 38.3 + - + +
41D THR* 3.1 25.1 + - - +
42D VAL 3.1 0.8 - - - -
43D GLU* 1.3 73.2 - - - +
45D ALA* 1.3 60.8 + - - +
47D SER* 3.5 7.1 + - - -
48D ALA* 3.0 27.9 + - - +
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Residues in contact with ALA 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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8D ILE* 3.8 29.9 - - + +
41D THR 3.2 4.2 + - - +
42D VAL 2.9 9.1 + - - +
44D GLN* 1.3 75.4 - - - +
46D ILE* 1.3 65.0 + - - +
48D ALA* 3.2 2.3 + - - +
49D ALA* 3.0 18.7 + - - +
170D VAL* 3.9 24.0 - - + -
199D ASN* 3.4 18.1 + - + -
201D VAL* 4.1 10.1 - - + -
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Residues in contact with ILE 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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42D VAL* 2.9 37.9 + - + +
43D GLU* 3.9 4.9 - - + +
45D ALA* 1.3 73.0 - - - +
47D SER* 1.3 52.6 + - - +
49D ALA* 3.0 3.4 + - - +
50D GLN* 2.7 33.4 + - - +
141D VAL* 4.3 11.4 - - + -
170D VAL* 4.2 17.3 - - + -
210D ALA 4.6 0.2 - - - +
211D LEU* 4.0 8.7 - - + -
214D ASP* 3.5 31.4 - - + +
216D ARG* 3.6 42.0 - - + +
217D VAL* 3.8 17.5 - - + -
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Residues in contact with SER 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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43D GLU* 2.5 25.6 + - - +
44D GLN* 3.8 7.4 - - - -
46D ILE* 1.3 75.4 - - - +
48D ALA* 1.3 58.4 + - - +
50D GLN* 3.8 3.5 - - - +
51D HIS* 2.9 30.7 + - - +
216D ARG* 3.1 22.4 + - - +
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Residues in contact with ALA 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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8D ILE* 4.0 9.6 - - + -
9D ASN* 3.7 38.6 - - + +
44D GLN 3.0 14.9 + - - +
45D ALA 3.5 7.9 - - - +
46D ILE 3.2 0.2 - - - -
47D SER* 1.3 78.3 - - - +
49D ALA* 1.3 56.3 + - - +
51D HIS* 3.5 5.6 + - - +
52D ALA* 3.1 28.2 + - - +
196D GLY* 3.9 5.0 - - - -
199D ASN* 4.2 2.9 - - - +
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Residues in contact with ALA 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 ALA 3.0 13.4 + - - +
46D ILE 3.4 7.0 - - - +
48D ALA* 1.3 73.7 - - - +
50D GLN* 1.3 65.8 + - - +
52D ALA 3.3 0.9 + - - -
53D PHE* 3.1 18.9 + - - +
141D VAL* 3.7 22.2 - - + -
168D CYS* 3.3 27.9 - - + +
169D PHE 4.5 1.3 - - - +
170D VAL* 4.2 5.2 - - + -
196D GLY 3.4 10.8 - - - -
199D ASN* 3.7 11.3 - - - +
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Residues in contact with GLN 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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46D ILE 2.7 19.4 + - - +
47D SER* 3.8 8.1 - - - +
49D ALA* 1.3 71.7 - - - +
51D HIS* 1.3 62.7 + - - +
53D PHE* 3.2 30.6 + - - +
54D PRO* 3.2 15.6 - - - +
140D GLY* 5.5 0.9 - - - -
141D VAL* 3.3 22.5 + - + +
216D ARG* 3.9 35.3 - - - +
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Residues in contact with HIS 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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9D ASN* 5.8 2.4 + - - +
47D SER 2.9 20.2 + - - +
48D ALA* 3.7 7.0 - - - +
49D ALA 3.2 0.2 - - - -
50D GLN* 1.3 78.0 - - - +
52D ALA* 1.3 59.5 + - - +
53D PHE 3.6 0.5 + - - -
54D PRO* 3.7 8.9 - - - +
55D THR* 5.2 1.7 + - - -
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Residues in contact with ALA 52 (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 ASN* 5.2 0.2 - - - +
48D ALA 3.1 16.5 + - - +
49D ALA 3.3 3.5 + - - +
51D HIS* 1.3 76.4 + - - +
53D PHE* 1.3 65.4 + - - +
54D PRO* 3.6 0.7 - - - -
55D THR* 3.5 9.7 + - - -
56D TRP* 3.4 19.1 + - - +
168D CYS* 3.8 1.8 - - - -
194D PRO* 5.7 1.3 - - + -
195D ASP 3.6 24.0 - - - +
196D GLY 3.8 1.1 - - - -
197D VAL* 3.8 23.5 - - + +
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Residues in contact with PHE 53 (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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49D ALA 3.1 10.5 + - - +
50D GLN* 3.2 24.7 + - - +
52D ALA* 1.3 73.9 - - - +
54D PRO* 1.3 82.4 - - + +
56D TRP* 2.9 3.3 + - - -
57D ARG* 2.7 53.5 + - + +
138D PRO* 3.7 14.6 - - + -
139D MET 4.4 2.7 - - - -
140D GLY* 3.4 47.6 - - - -
166D GLY 3.3 26.2 - - - -
168D CYS* 3.6 13.5 - - + -
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Residues in contact with PRO 54 (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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50D GLN* 3.2 17.0 - - - +
51D HIS* 3.7 11.2 - - - +
52D ALA 3.7 0.4 - - - -
53D PHE* 1.3 103.5 - - + +
55D THR* 1.3 62.5 + - + +
57D ARG* 3.5 17.0 - - + +
58D ASN* 3.5 19.2 + - - -
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Residues in contact with THR 55 (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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51D HIS 5.2 1.4 + - - -
52D ALA* 3.5 11.6 + - - -
53D PHE 2.9 0.6 + - - -
54D PRO* 1.3 80.6 - - + +
56D TRP* 1.3 56.9 + - - +
58D ASN* 3.8 5.0 + - - +
59D THR* 2.6 30.5 + - - -
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Residues in contact with TRP 56 (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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52D ALA 3.4 15.9 + - - +
53D PHE* 2.9 4.8 + - - +
55D THR* 1.3 79.2 + - - +
57D ARG* 1.3 63.7 - - - +
58D ASN 3.2 1.0 + - - -
59D THR* 3.2 30.9 + - + -
63D LYS* 5.4 1.6 - - + -
64D ARG* 3.2 59.7 + - + +
67D VAL* 4.0 11.4 - - + -
163D ILE* 2.9 37.8 + - + -
164D VAL* 5.1 0.2 - - - -
166D GLY 3.6 15.7 - - - -
167D ASN 3.2 23.5 + - - -
168D CYS* 4.4 1.3 - - - -
193D LEU* 3.6 13.0 - - + -
194D PRO* 3.7 31.4 - - + -
197D VAL* 3.5 22.8 - - + +
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Residues in contact with ARG 57 (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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124A ARG* 3.3 23.8 + - - +
427C ASP* 2.9 35.4 + - - -
428C ASN* 3.4 25.8 - - - +
430C GLN* 4.2 14.7 - - - +
452C TRP* 5.5 1.0 - - - -
53D PHE* 2.7 47.7 + - + +
54D PRO* 3.5 10.3 - - - +
56D TRP* 1.3 73.4 - - - +
58D ASN* 1.3 67.9 + - - +
59D THR 4.2 0.2 - - - +
64D ARG* 3.2 16.0 + - - +
137D GLN* 3.2 29.7 + - - +
138D PRO* 4.0 18.2 + - + +
166D GLY 3.8 12.2 + - - -
473D LYS* 6.3 0.4 - - - +
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Residues in contact with ASN 58 (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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124A ARG* 3.1 22.5 + - - -
125A ASN* 3.5 20.4 + - - +
128A PRO* 5.4 3.5 - - - +
427C ASP* 4.2 5.3 - - - +
428C ASN* 4.7 9.3 - - - +
54D PRO 3.5 17.8 + - - +
55D THR* 3.8 5.5 + - - +
56D TRP 3.2 0.4 - - - -
57D ARG* 1.3 86.7 + - - +
59D THR* 1.3 65.7 + - - +
60D PRO* 3.5 7.4 - - - +
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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