Contacts of the helix formed by residues 42 - 59 (chain A) in PDB entry 4AW9
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 ASN 42 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A SER* 3.3 23.4 + - - +
38A ASN 3.0 27.3 + - - +
39A GLY 3.0 6.6 + - - +
41A TYR* 1.3 83.4 - - - +
43A TYR* 1.3 66.0 + - - +
44A ARG* 2.9 18.7 + - - +
45A HIS* 3.1 18.7 + - - +
46A GLN* 4.1 5.1 + - - -
74A ILE* 4.9 0.9 - - - -
148A HIS* 2.8 35.8 + - - -
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Residues in contact with TYR 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A GLY 3.6 1.8 + - - -
40A TRP* 3.1 58.4 + + - +
41A TYR 3.4 1.0 - - - -
42A ASN* 1.3 74.7 - - - +
44A ARG* 1.3 65.1 - - - +
45A HIS 3.2 0.7 + - - -
46A GLN* 3.3 6.6 + - - +
47A ALA* 3.1 27.9 + - + -
74A ILE* 3.6 28.3 - - + +
80A ASN* 5.0 2.2 - - - -
85A ILE 4.2 1.1 + - - -
86A VAL* 3.4 12.3 - - + -
87A ILE* 2.9 50.5 + - - +
225A ARG* 3.8 12.2 + - - -
227A THR* 3.6 15.9 - - + +
228A TYR 3.6 10.3 - - - +
229A LEU* 3.6 16.8 - - + -
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Residues in contact with ARG 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A TYR 3.1 27.3 + - - -
42A ASN* 2.9 5.8 + - - +
43A TYR* 1.3 79.3 - - - +
45A HIS* 1.3 65.1 + - + +
47A ALA* 3.3 1.4 + - - +
48A ASP* 2.8 40.0 + - - +
148A HIS* 3.4 25.9 - - - -
218A ALA* 3.5 18.5 - - - +
227A THR* 5.1 0.2 + - - -
228A TYR* 3.4 23.7 + - - +
229A LEU 3.6 11.9 - - - -
230A GLY 3.4 26.5 - - - +
231A ASP* 3.1 18.0 + - - +
302I VAL* 3.8 14.4 - - - +
303I ALA 3.5 9.7 + - - -
304I ASP* 2.8 30.1 + - - -
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Residues in contact with HIS 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ALA* 3.6 8.6 - - + +
37A SER* 2.8 28.7 + - - +
42A ASN* 3.1 9.3 + - - +
44A ARG* 1.3 102.0 - - + +
46A GLN* 1.3 57.2 + - - +
48A ASP* 3.3 4.1 - - - +
49A ALA 3.1 19.8 + - - -
146A THR* 3.3 38.8 - - - +
147A ASP* 3.2 25.1 + - - -
148A HIS* 3.9 14.1 - - - -
187A GLU* 5.1 0.4 - - + -
231A ASP* 3.4 20.6 + - - -
304I ASP* 3.0 23.7 + - - -
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Residues in contact with GLN 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ALA* 3.8 20.9 - - + -
37A SER 3.5 19.0 + - - +
38A ASN* 3.9 5.3 - - - +
39A GLY 5.2 0.2 + - - -
42A ASN 4.1 5.1 + - - +
43A TYR 3.3 7.4 + - - +
45A HIS* 1.3 73.9 - - + +
47A ALA* 1.3 60.2 + - - +
49A ALA* 3.3 3.5 + - - +
50A CYS* 2.9 36.9 + - - -
70A MET* 4.1 12.1 - - + +
71A TYR* 3.8 5.6 + - - +
72A ASP* 2.8 33.3 + - - -
73A ASP* 2.8 25.9 + - - -
74A ILE* 3.5 25.0 + - + +
86A VAL* 5.0 1.1 - - + -
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Residues in contact with ALA 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A TYR* 3.1 21.4 + - + +
44A ARG 3.6 3.1 - - - +
46A GLN* 1.3 75.7 - - - +
48A ASP* 1.3 59.8 + - - +
50A CYS* 3.5 2.6 + - - +
51A HIS* 3.1 24.9 + - - +
86A VAL* 3.7 16.8 - - + +
87A ILE 3.5 18.6 - - - +
88A ASN* 3.6 7.8 - - - +
95A VAL* 3.9 1.6 - - - +
229A LEU 3.3 24.7 - - - +
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Residues in contact with ASP 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ARG 2.8 20.4 + - - +
45A HIS 3.3 9.0 - - - +
47A ALA* 1.3 72.5 - - - +
49A ALA* 1.3 57.4 + - - +
51A HIS 3.4 0.3 + - - -
52A ALA* 2.9 25.3 + - - +
88A ASN* 2.9 22.3 + - - +
144A TYR* 3.3 16.2 - - - +
146A THR* 3.2 13.5 + - + -
230A GLY* 3.5 9.4 - - - -
231A ASP* 2.5 27.4 + - - +
234A SER* 3.4 20.3 + - - -
235A VAL* 4.3 0.9 - - - +
238A MET* 3.3 15.6 - - + +
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Residues in contact with ALA 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ILE* 3.6 30.3 - - + +
35A ALA* 3.9 18.6 - - + +
45A HIS 3.1 11.4 + - - +
46A GLN 3.3 7.4 + - - +
48A ASP* 1.3 79.0 - - - +
50A CYS* 1.3 63.7 + - - +
52A ALA* 3.3 5.5 + - - +
53A TYR* 3.1 19.8 + - - +
68A VAL* 5.7 0.2 - - - +
69A MET 5.3 0.4 - - - +
70A MET* 3.8 18.0 - - + +
144A TYR* 4.4 3.1 - - - -
146A THR* 4.6 2.0 - - + -
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Residues in contact with CYS 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A GLN* 2.9 26.4 + - - +
47A ALA* 3.8 2.0 - - - +
49A ALA* 1.3 73.2 - - - +
51A HIS* 1.3 66.2 + - - +
53A TYR* 3.2 5.2 + - - +
54A GLN* 3.2 25.1 + - - +
70A MET* 3.6 20.6 - - - -
86A VAL* 5.0 4.5 - - - -
95A VAL* 3.4 31.1 - - + +
96A TYR* 3.9 24.0 - - - -
99A VAL* 3.9 17.9 - - + -
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Residues in contact with HIS 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ALA 3.1 18.0 + - - +
48A ASP 3.6 3.4 - - - +
50A CYS* 1.3 74.9 - - - +
52A ALA* 1.3 63.4 + - - +
54A GLN* 3.1 14.9 + - + +
55A ILE* 3.2 20.8 + - + +
88A ASN* 2.7 37.8 + - + +
89A ARG* 6.5 2.2 - - + -
95A VAL* 3.9 19.4 - - + +
235A VAL* 5.4 0.7 - - - -
238A MET* 3.6 22.2 - - + +
239A GLU* 4.3 12.3 - - + -
242A ASP* 2.6 32.6 + - - -
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Residues in contact with ALA 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ILE* 3.8 12.3 - - + -
48A ASP 2.9 14.3 + - - +
49A ALA 3.4 9.2 - - - +
50A CYS 3.3 0.2 - - - -
51A HIS* 1.3 77.6 - - - +
53A TYR* 1.3 62.3 + - - +
55A ILE* 3.5 8.0 + - - +
56A ILE* 3.0 27.5 + - + +
142A PHE* 6.2 0.4 - - + -
144A TYR* 3.7 27.8 - - + -
237A TRP* 4.2 8.7 - - + -
238A MET* 3.4 10.3 - - - -
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Residues in contact with TYR 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ILE* 3.7 11.4 - - + +
49A ALA 3.1 13.2 + - - +
50A CYS 3.2 6.9 + - - +
52A ALA* 1.3 76.4 - - - +
54A GLN* 1.3 69.3 + - - +
56A ILE* 3.1 3.6 + - + +
57A HIS* 2.8 57.7 + + + +
63A ASP* 2.7 33.2 + - - -
66A ILE* 3.9 27.1 - - + -
68A VAL* 4.4 2.7 - - + -
97A GLN 5.1 0.2 - - - -
98A GLY* 3.2 30.7 + - - -
99A VAL* 3.8 27.4 - - + -
100A PRO* 3.4 20.2 - - + -
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Residues in contact with GLN 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A CYS 3.3 10.5 - - - +
51A HIS* 3.1 11.3 + - + +
53A TYR* 1.3 86.3 - - - +
55A ILE* 1.3 53.5 + - - +
57A HIS* 3.4 10.9 + - - +
58A ARG* 2.8 38.2 + - - +
94A ASP 5.1 2.2 + - - +
95A VAL* 2.7 44.9 + - + +
97A GLN 3.0 25.4 + - - +
99A VAL* 3.7 9.5 - - - +
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Residues in contact with ILE 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A HIS* 3.2 18.7 + - + +
52A ALA* 3.7 6.1 - - - +
54A GLN* 1.3 77.0 - - + +
56A ILE* 1.3 64.1 + - + +
58A ARG* 3.3 4.4 + - - +
59A ASN* 2.7 45.6 + - - +
237A TRP* 4.3 5.2 - - + -
238A MET* 3.6 52.3 - - + +
241A SER* 3.9 22.4 - - - +
242A ASP* 3.3 19.3 - - - +
246A LEU* 4.8 0.2 - - + -
284A GLN* 3.9 15.9 - - + +
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Residues in contact with ILE 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A VAL* 3.8 33.9 - - + -
33A ILE* 4.2 4.5 - - + -
52A ALA 3.0 17.7 - - - +
53A TYR* 3.1 7.7 + - - +
55A ILE* 1.3 77.6 - - + +
57A HIS* 1.3 61.3 + - - +
59A ASN 3.4 8.7 + - - -
60A GLY 3.6 0.5 + - - -
61A ILE* 3.4 39.4 + - + +
66A ILE* 3.7 19.7 - - + -
142A PHE* 4.2 15.5 - - + -
237A TRP* 5.6 2.2 - - + -
284A GLN* 3.7 38.2 - - + +
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Residues in contact with HIS 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A TYR* 2.8 54.5 + + + +
54A GLN* 3.9 13.5 - - - +
56A ILE* 1.3 71.7 - - - +
58A ARG* 1.3 67.8 + - - +
59A ASN 3.3 0.7 + - - -
60A GLY* 3.5 9.9 + - - -
61A ILE 4.1 12.5 + - - +
62A PRO* 6.1 0.6 - - - +
63A ASP* 4.3 7.4 + - - -
66A ILE* 5.2 0.2 - - - -
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Residues in contact with ARG 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A GLN 2.8 20.6 + - - +
55A ILE* 3.6 7.9 - - - +
56A ILE 3.3 0.2 - - - -
57A HIS* 1.3 79.9 - - + +
59A ASN* 1.3 68.7 + - - +
60A GLY 3.5 1.1 + - - -
317A SO4 2.1 46.9 + - - -
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Residues in contact with ASN 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ILE* 2.7 33.9 + - - +
56A ILE 3.4 0.8 + - - -
57A HIS 3.2 0.6 - - - -
58A ARG* 1.3 89.8 + - - +
60A GLY* 1.3 54.8 - - - +
61A ILE 3.7 2.2 - - - -
241A SER 5.1 2.6 + - - -
246A LEU* 3.4 32.4 - - - +
281A MET* 3.4 24.6 - - - +
284A GLN 3.4 19.0 + - - +
285A GLY* 3.3 6.0 - - - -
286A MET 3.2 18.2 + - - -
288A ARG* 4.0 3.0 + - - -
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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
------------------------------------------------------------
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