Contacts of the helix formed by residues 55 - 71 (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 ARG 55 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D LEU 3.2 21.6 + - - -
14D SER* 3.5 16.8 + - - +
16D LEU* 2.8 30.7 + - - +
51D ALA* 3.9 14.1 - - + +
52D LYS* 2.9 24.1 + - + +
54D ASN* 1.3 91.1 - - - +
56D LYS* 1.3 60.9 + - - +
57D LEU 3.2 2.9 - - - -
58D THR* 2.9 33.9 + - - +
59D PHE* 3.3 34.3 + - + -
201D UNX 4.4 1.1 - - - -
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Residues in contact with LYS 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D LEU* 2.8 47.0 + - + +
49D ARG 3.1 9.5 + - - -
51D ALA* 2.9 21.6 + - + +
52D LYS 3.5 10.1 - - - +
53D SER* 3.5 22.7 + - - +
55D ARG* 1.3 78.4 - - - +
57D LEU* 1.3 61.6 + - - +
59D PHE* 3.2 16.2 + - - +
60D LEU* 3.3 13.2 + - - +
91D HIS* 2.9 33.1 + - + +
92D VAL* 4.1 18.2 - - + -
95D GLU* 3.8 28.9 + - + -
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Residues in contact with LEU 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D SER 4.8 1.6 + - - -
54D ASN 5.0 1.3 - - - +
55D ARG 3.2 1.0 - - - +
56D LYS* 1.3 77.2 - - - +
58D THR* 1.3 57.4 + - - +
60D LEU* 3.1 12.8 + - + +
61D TYR* 2.9 61.0 + - + +
92D VAL* 5.1 3.0 - - + +
206D UNX 4.4 19.1 - - - +
103E PRO* 3.6 35.7 - - + -
104E LEU* 3.6 28.9 - - + -
107E LEU* 5.1 1.6 - - + -
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Residues in contact with THR 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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16D LEU* 4.2 14.2 - - + +
17D SER* 3.2 33.4 - - - +
18D ASN* 3.8 12.9 - - - +
23D VAL* 4.0 11.6 - - + +
55D ARG* 2.9 17.5 + - - -
57D LEU* 1.3 79.2 - - - +
59D PHE* 1.3 56.9 + - - +
61D TYR* 3.2 11.7 + - + +
62D LEU* 3.0 27.2 + - - +
201D UNX 4.2 5.4 + - - -
206D UNX 3.6 19.6 + - - -
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Residues in contact with PHE 59 (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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13D LEU* 4.0 33.7 - - + -
16D LEU* 4.8 7.4 - - + -
44D TRP* 2.9 46.6 + + + +
47D GLU* 3.7 25.4 - - + -
48D LEU* 3.6 37.9 - - + -
51D ALA* 3.7 22.9 - - + -
55D ARG* 3.5 34.5 - - - -
56D LYS* 3.2 9.7 + - - +
58D THR* 1.3 80.1 - - - +
60D LEU* 1.3 56.7 + - - +
62D LEU* 3.4 4.9 + - - +
63D ALA 3.0 15.1 + - - -
205D UNX 4.3 2.5 - - - -
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Residues in contact with LEU 60 (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* 4.1 23.8 - - + -
48D LEU* 4.9 1.6 - - + -
56D LYS 3.3 8.2 + - - +
57D LEU* 3.1 10.6 + - + +
59D PHE* 1.3 75.8 - - - +
61D TYR* 1.3 60.0 + - - +
63D ALA* 3.4 3.0 + - + +
64D ASN* 2.9 27.2 + - - +
85D LEU* 4.6 3.6 - - + -
88D ALA* 4.5 8.5 - - + -
89D PHE* 3.9 35.7 - - + -
92D VAL* 3.8 26.5 - - + -
104E LEU* 3.5 31.9 - - + -
107E LEU* 4.0 15.1 - - + +
111E TRP* 4.8 2.4 - - + -
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Residues in contact with TYR 61 (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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1611C BTN 5.5 0.5 + - - -
18D ASN* 6.4 2.0 - - + -
23D VAL* 4.1 5.4 - - + -
57D LEU* 2.9 52.9 + - + +
58D THR* 3.6 15.0 - - + +
59D PHE 3.2 0.2 - - - -
60D LEU* 1.3 75.6 - - - +
62D LEU* 1.3 59.7 + - - +
64D ASN* 3.3 3.5 + - - +
65D ASP* 2.9 28.9 + - - +
103E PRO* 4.1 11.6 + - - +
107E LEU* 4.1 21.3 - - + -
1622F TYR* 3.6 42.6 - + + -
1624F PRO* 3.8 35.9 - - + +
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Residues in contact with LEU 62 (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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13D LEU* 3.7 18.6 - - + -
16D LEU* 4.1 10.1 - - + -
23D VAL* 3.6 33.0 - - + +
26D LEU* 3.6 31.6 - - + -
27D SER* 3.6 22.0 - - - +
30D LEU* 4.0 13.9 - - + -
44D TRP* 4.0 15.5 - - + +
58D THR 3.0 12.6 + - - +
59D PHE* 3.4 7.6 + - - +
61D TYR* 1.3 77.0 - - - +
63D ALA* 1.3 62.8 + - - +
65D ASP* 3.2 1.0 + - - -
66D VAL* 2.9 25.3 + - + +
81D PHE* 6.3 0.2 - - + -
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Residues in contact with ALA 63 (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* 3.6 19.5 - - + +
59D PHE 3.0 6.7 + - - -
60D LEU* 3.6 9.4 - - + +
62D LEU* 1.3 75.2 - - - +
64D ASN* 1.3 57.9 + - - +
66D VAL* 3.7 0.7 - - - +
67D ILE* 2.8 42.9 + - + +
81D PHE* 3.5 40.8 - - + -
85D LEU* 4.8 5.2 - - + -
111E TRP* 5.3 1.8 - - + -
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Residues in contact with ASN 64 (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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60D LEU 2.9 14.5 + - - +
61D TYR* 3.4 9.6 - - - +
63D ALA* 1.3 75.2 - - - +
65D ASP* 1.3 56.6 + - - +
67D ILE* 3.9 1.1 - - - +
68D GLN* 2.7 50.2 + - - +
107E LEU* 3.8 15.9 - - + +
110E ILE* 4.8 0.2 - - - +
111E TRP* 2.7 41.2 + - + +
1622F TYR* 3.0 25.9 + - - -
1624F PRO* 3.1 25.8 + - - +
1627F PRO* 4.2 1.2 - - - +
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Residues in contact with ASP 65 (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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20D GLN* 4.9 0.5 + - - -
23D VAL* 4.1 6.3 - - + -
24D GLN* 4.2 11.8 - - - +
27D SER* 2.7 30.3 + - - +
61D TYR 2.9 11.9 + - - +
62D LEU 3.2 4.0 + - - +
64D ASN* 1.3 75.5 - - - +
66D VAL* 1.3 60.4 + - - +
68D GLN* 4.3 0.2 - - - +
69D ASN* 3.0 53.5 + - - +
1622F TYR* 2.6 39.3 + - + +
1626F SER* 4.0 1.2 + - - -
1627F PRO* 3.5 15.1 - - - +
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Residues in contact with VAL 66 (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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27D SER* 3.6 29.2 - - - +
30D LEU* 3.9 22.9 - - + -
31D ILE* 4.0 6.0 - - + +
62D LEU* 2.9 22.1 + - + +
63D ALA* 3.8 3.6 - - - +
65D ASP* 1.3 76.5 - - - +
67D ILE* 1.3 57.8 + - - +
70D SER* 2.8 35.5 + - - -
77D PHE* 3.5 47.1 - - + -
81D PHE* 3.9 11.9 - - + -
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Residues in contact with ILE 67 (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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63D ALA* 2.8 32.7 + - + +
64D ASN* 3.9 2.9 - - - +
66D VAL* 1.3 71.7 - - - +
68D GLN* 1.3 65.5 + - - +
70D SER* 2.9 20.4 + - - -
71D LYS* 3.5 12.8 + - - +
77D PHE* 4.4 4.3 - - - +
78D THR* 4.1 15.9 - - - +
81D PHE* 3.5 35.4 - - + -
85D LEU* 4.0 10.8 - - + -
111E TRP* 4.3 8.7 - - + -
116E VAL* 3.5 28.0 - - + -
117E TYR* 3.5 27.6 - - + +
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Residues in contact with GLN 68 (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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64D ASN* 2.7 44.4 + - - +
67D ILE* 1.3 76.8 - - - +
69D ASN* 1.3 62.6 + - - +
71D LYS* 3.6 20.9 + - - +
72D ARG 4.9 0.5 + - - -
110E ILE* 4.0 10.9 - - - +
111E TRP* 4.3 2.6 - - - +
114E ARG* 2.9 36.5 + - - +
116E VAL* 4.1 20.9 - - + -
1624F PRO 3.3 18.4 + - - -
1627F PRO* 3.6 18.8 - - + +
1629F TYR* 3.7 27.1 - - + +
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Residues in contact with ASN 69 (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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24D GLN* 6.2 0.2 - - - +
27D SER* 4.4 0.8 + - - -
28D LEU* 6.3 1.9 - - - +
31D ILE* 3.4 20.6 - - + +
65D ASP* 3.0 46.2 + - - +
68D GLN* 1.3 76.4 - - - +
70D SER* 1.3 63.5 + - - +
71D LYS 3.3 0.5 + - - -
72D ARG* 3.9 21.8 + - - +
73D LYS* 4.2 2.9 - - - +
1627F PRO* 4.2 17.1 - - - +
1628F SER* 4.5 9.5 + - - -
1629F TYR* 5.9 0.5 - - - +
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Residues in contact with SER 70 (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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31D ILE* 3.6 11.0 - - - +
34D ARG* 6.1 1.3 - - - -
66D VAL 2.8 20.7 + - - -
67D ILE* 2.9 17.8 + - - -
69D ASN* 1.3 73.1 - - - +
71D LYS* 1.3 54.8 + - - +
72D ARG 3.2 0.2 - - - -
73D LYS* 2.7 35.2 + - - +
74D GLY 3.1 15.6 + - - +
77D PHE* 3.3 39.4 - - - +
78D THR* 4.4 3.6 + - - -
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Residues in contact with LYS 71 (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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67D ILE* 3.5 14.6 - - - +
68D GLN* 3.7 10.1 - - - +
69D ASN 3.2 1.4 - - - -
70D SER* 1.3 80.5 + - - +
72D ARG* 1.3 58.3 + - - +
73D LYS 3.1 4.0 + - - -
74D GLY* 3.6 16.7 + - - +
75D PRO* 6.1 1.1 - - + -
78D THR* 3.0 36.2 + - - +
115E SER 4.9 1.0 + - - -
116E VAL* 3.3 43.6 + - - +
1629F TYR* 3.1 45.7 + - + +
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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
------------------------------------------------------------
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