Contacts of the helix formed by residues 72 - 88 (chain D) in PDB entry 4NH1
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 ILE 72 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D HIS* 4.6 21.9 - - + +
48D GLN* 4.2 25.1 - - + +
49D ALA* 5.0 2.1 - - - +
52D MET* 3.8 22.7 - - + -
66D PRO 5.2 2.0 - - - +
68D GLN 3.8 7.2 - - - +
69D SER* 2.7 29.1 + - - +
70D ASP 3.2 0.2 - - - -
71D LEU* 1.3 91.3 - - + +
73D GLU* 1.3 60.6 + - - +
74D GLN 3.3 0.9 - - - -
75D ALA* 3.0 7.1 + - - +
76D ALA* 2.8 26.3 + - - +
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Residues in contact with GLU 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D TRP* 3.1 37.6 + - - -
12D TRP* 4.2 14.2 - - - -
52D MET* 3.6 22.0 - - + +
69D SER* 2.3 37.3 + - - +
70D ASP* 5.1 0.9 - - - +
72D ILE* 1.3 65.6 - - - +
74D GLN* 1.3 58.6 + - + +
75D ALA 3.0 4.5 - - - -
76D ALA* 3.1 14.6 + - - +
77D GLU* 3.0 30.7 + - - +
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Residues in contact with GLN 74 (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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69D SER 3.7 1.8 + - - -
70D ASP* 3.2 40.3 + - - +
72D ILE 3.3 0.2 - - - -
73D GLU* 1.3 78.1 - - + +
75D ALA* 1.3 58.2 + - - +
76D ALA 3.4 0.2 - - - -
77D GLU* 3.8 31.5 - - - +
78D MET* 3.9 13.2 + - - +
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Residues in contact with ALA 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D VAL* 4.8 3.8 - - - +
44D PRO* 4.0 31.7 - - + +
45D HIS* 4.5 1.6 - - + +
49D ALA* 3.6 11.5 - - + +
70D ASP 4.4 0.2 + - - -
71D LEU* 3.4 22.9 - - - +
72D ILE* 3.0 12.5 + - - +
74D GLN* 1.3 77.5 - - - +
76D ALA* 1.3 62.0 + - - +
77D GLU 3.3 0.7 - - - -
78D MET* 3.6 10.7 - - - +
79D LEU* 3.5 14.2 + - - +
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Residues in contact with ALA 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D TRP* 4.1 3.8 - - + -
48D GLN 4.7 0.2 - - - +
49D ALA* 3.6 30.5 - - - +
52D MET* 4.0 18.2 - - - -
53D ILE* 3.8 15.8 - - + +
72D ILE 2.8 10.9 + - - +
73D GLU 3.1 9.6 + - - +
75D ALA* 1.3 77.7 - - - +
77D GLU* 1.3 62.2 + - - +
78D MET 3.2 0.4 - - - -
79D LEU* 3.4 2.9 + - - +
80D TYR* 3.2 23.6 + - - +
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Residues in contact with GLU 77 (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 TRP* 4.4 11.0 - - + -
12D TRP* 5.2 5.5 - - - -
13D PHE* 3.9 36.8 - - + -
16D LEU* 5.7 1.9 - - - +
73D GLU* 3.0 30.5 + - - +
74D GLN* 3.8 29.8 - - - +
76D ALA* 1.3 77.5 - - - +
78D MET* 1.3 62.4 + - - +
80D TYR* 4.0 1.5 - - - +
81D GLY* 3.1 20.8 + - - -
158D TYR* 4.5 6.4 - - + -
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Residues in contact with MET 78 (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 GLN* 3.5 24.0 - - + +
43D VAL* 3.7 15.7 - - + -
44D PRO* 4.1 18.2 - - + -
74D GLN 3.9 8.4 + - - +
75D ALA* 3.6 15.1 + - - +
76D ALA 3.2 0.4 - - - -
77D GLU* 1.3 80.4 - - - +
79D LEU* 1.3 60.4 + - - +
81D GLY 3.5 0.7 + - - -
82D LEU* 3.2 34.1 + - + +
128D PRO* 4.6 24.5 - - + -
158D TYR* 3.5 24.9 - - + +
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Residues in contact with LEU 79 (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 LEU* 5.8 0.2 - - + -
39D LEU* 4.2 15.0 - - + -
43D VAL* 3.8 28.7 - - + +
46D TYR* 4.1 20.2 - - + +
49D ALA* 3.6 44.0 - - + +
50D LEU* 3.6 18.4 - - + +
53D ILE* 4.4 2.9 - - + -
75D ALA 3.5 3.3 + - - +
76D ALA 3.4 8.2 + - - +
77D GLU 3.3 0.6 - - - -
78D MET* 1.3 76.3 - - - +
80D TYR* 1.3 60.9 + - - +
82D LEU* 3.0 6.5 + - + +
83D ILE* 2.9 50.9 + - + +
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Residues in contact with TYR 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D TRP* 4.0 16.4 - + + -
10D ILE* 3.3 25.1 - - + +
13D PHE* 3.8 37.2 - + - -
14D CYS* 3.3 14.5 - - - -
22D PHE* 4.3 10.3 - + - -
23D CYS 2.8 24.1 + - - -
25D VAL* 3.1 35.1 + - + -
30D ILE* 4.7 7.2 - - + -
53D ILE* 4.0 22.6 - - + +
76D ALA 3.2 13.5 + - - +
77D GLU* 4.2 2.5 - - - +
79D LEU* 1.3 79.4 - - - +
81D GLY* 1.3 58.7 + - - +
83D ILE* 3.7 6.7 - - + +
84D HIS* 2.9 30.8 + - + +
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Residues in contact with GLY 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D PHE* 4.5 7.6 - - - -
77D GLU 3.1 16.6 + - - -
79D LEU 3.1 0.4 - - - -
80D TYR* 1.3 78.4 - - - +
82D LEU* 1.3 60.4 + - - +
84D HIS* 3.3 6.8 + - - +
85D ALA 3.3 15.6 + - - -
158D TYR* 3.3 43.6 - - - -
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Residues in contact with LEU 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D LEU* 4.6 17.7 - - + -
42D GLN* 3.9 28.7 - - + +
43D VAL* 3.7 28.7 - - + -
78D MET* 3.2 18.1 + - + +
79D LEU* 3.0 8.1 + - + +
81D GLY* 1.3 72.0 - - - +
83D ILE* 1.3 65.1 + - - +
85D ALA* 3.2 19.4 + - + +
86D ARG* 3.4 13.3 + - - +
126D ASP 5.6 1.1 - - - +
128D PRO* 4.0 19.1 - - + -
157D ALA* 4.2 9.9 - - + +
158D TYR* 3.8 20.6 - - + -
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Residues in contact with ILE 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D VAL* 4.6 8.5 - - + -
29D TYR* 4.1 23.7 - - + -
30D ILE* 4.4 19.7 - - + -
35D ASN 5.7 2.0 - - - +
36D LEU* 4.4 25.4 - - + -
39D LEU* 4.5 10.3 - - + -
50D LEU* 5.3 0.2 - - + -
53D ILE* 4.1 19.1 - - + -
79D LEU* 2.9 46.8 + - + +
80D TYR* 3.7 6.1 - - + +
82D LEU* 1.3 75.6 - - - +
84D HIS* 1.3 58.9 + - - +
86D ARG* 3.2 10.1 + - - +
87D TYR* 2.9 25.6 + - - +
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Residues in contact with HIS 84 (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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22D PHE* 4.1 16.1 - + + -
23D CYS* 3.0 59.9 + - - -
25D VAL* 4.4 11.4 - - + -
80D TYR* 2.9 21.3 + - + +
81D GLY* 3.4 9.4 - - - +
82D LEU 3.2 0.4 - - - -
83D ILE* 1.3 77.9 - - - +
85D ALA* 1.3 60.5 + - - +
87D TYR* 4.1 4.9 - + - -
88D ILE* 3.1 41.5 + - + +
97D MET* 4.3 5.2 - - - -
158D TYR 3.2 17.3 + - - +
159D PHE* 3.9 25.5 - + - -
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Residues in contact with ALA 85 (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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81D GLY 3.3 3.6 + - - +
82D LEU* 3.2 12.7 + - + +
83D ILE 3.1 0.4 - - - -
84D HIS* 1.3 80.8 - - - +
86D ARG* 1.3 61.2 + - + +
87D TYR 3.5 0.2 + - - -
88D ILE* 3.6 11.1 - - - +
89D LEU* 3.4 23.3 - - - +
157D ALA 3.6 23.3 - - - +
158D TYR 3.6 12.8 + - - +
159D PHE 4.3 7.8 - - - +
160D GLY* 4.6 3.9 - - - +
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Residues in contact with ARG 86 (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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71B LYS* 5.1 12.5 + - - +
72B PRO* 5.2 11.7 - - - +
29D TYR* 3.2 19.8 + - + +
35D ASN* 3.2 28.1 + - - -
36D LEU* 3.8 3.0 - - - +
37D THR* 3.0 36.6 + - - +
38D GLY* 4.5 3.6 + - - -
39D LEU* 3.4 30.9 - - - +
42D GLN* 5.0 0.8 + - - -
82D LEU 3.4 11.7 + - - +
83D ILE* 3.2 9.5 + - - +
85D ALA* 1.3 78.3 - - + +
87D TYR* 1.3 61.8 + - - +
89D LEU* 3.6 19.2 + - + +
90D THR* 3.7 8.7 - - - +
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Residues in contact with TYR 87 (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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23D CYS* 4.0 16.2 - - - -
25D VAL* 4.0 20.6 - - + -
26D ASP* 2.9 31.5 + - + -
29D TYR* 3.6 45.3 - + + -
83D ILE 2.9 17.9 + - - +
84D HIS* 3.7 6.7 - + - +
85D ALA 3.2 0.4 - - - -
86D ARG* 1.3 74.2 - - - +
88D ILE* 1.3 59.2 + - + +
89D LEU 3.0 6.6 + - - -
90D THR* 2.6 31.5 + - - -
92D ARG* 3.7 8.9 - - + +
93D GLY* 3.4 24.2 - - - -
96D GLN* 2.4 42.0 + - - -
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Residues in contact with ILE 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D CYS* 4.0 6.7 - - - -
84D HIS* 3.1 47.5 + - + +
85D ALA 3.6 10.3 - - - +
87D TYR* 1.3 76.5 - - + +
89D LEU* 1.3 58.2 + - + +
90D THR 3.4 0.2 - - - -
93D GLY* 4.2 7.2 - - - +
94D ILE* 3.3 16.9 - - - +
97D MET* 3.7 17.5 - - + -
159D PHE* 3.2 41.3 - - + +
163D PHE* 3.2 47.2 - - + -
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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
------------------------------------------------------------
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