Contacts of the helix formed by residues 19 - 38 (chain A) in PDB entry 3NT7
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 TRP 19 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A TYR* 4.3 4.7 - - + -
16A HIS* 2.9 14.7 + - + +
18A ASP* 1.3 78.5 - - + +
20A GLU* 1.3 64.5 + - - +
21A PRO* 3.4 2.7 - - - -
22A VAL* 3.1 31.3 + - + +
23A MET* 3.4 22.5 - - - +
52A GLN 4.1 5.4 - - - -
53A LEU* 3.0 50.6 + - + +
55A GLN 2.8 24.8 + - - -
57A LEU* 3.7 25.8 - - + +
117A ILE* 4.0 13.2 - - + -
119A TRP* 3.7 20.6 - + - -
144A LEU* 4.3 13.2 - - + -
147A HIS* 3.9 21.1 - + - -
148A ILE* 3.6 32.3 - - + -
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Residues in contact with GLU 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A ASN* 4.5 6.4 - - - +
15A TYR* 2.7 36.6 + - - -
16A HIS 4.1 1.6 + - - -
17A ASP* 3.0 21.1 + - - +
19A TRP* 1.3 76.2 - - - +
21A PRO* 1.4 69.6 - - + +
22A VAL 3.1 1.7 + - - -
23A MET* 3.3 13.3 + - - +
24A SER* 4.5 2.9 + - - -
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Residues in contact with PRO 21 (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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17A ASP 4.5 0.7 - - - +
18A ASP 3.8 11.2 - - - +
19A TRP 3.5 4.3 - - - -
20A GLU* 1.4 93.5 - - + +
22A VAL* 1.3 60.1 + - + +
24A SER* 5.2 3.8 + - - -
25A GLN* 5.5 4.2 + - - +
147A HIS* 4.0 19.7 - - + +
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Residues in contact with VAL 22 (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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19A TRP* 3.2 30.1 - - + +
21A PRO* 1.3 80.6 - - + +
23A MET* 1.3 62.9 + - - +
24A SER 3.4 2.0 - - - -
25A GLN* 3.5 5.0 + - - +
26A LEU* 2.8 28.3 + - - +
143A LEU* 3.5 37.4 - - + +
144A LEU* 3.8 21.5 - - + -
147A HIS* 3.8 32.3 - - + +
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Residues in contact with MET 23 (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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4A VAL* 3.8 23.3 - - + -
13A ILE* 3.9 19.1 - - + -
15A TYR* 3.6 55.9 - - + +
19A TRP* 3.4 22.7 - - - +
20A GLU* 3.3 9.6 + - - +
22A VAL* 1.3 82.3 - - - +
24A SER* 1.3 66.6 + - - +
26A LEU* 3.2 16.9 + - + +
27A VAL* 3.0 29.6 + - - +
53A LEU* 4.0 19.7 - - + -
144A LEU* 5.8 0.2 - - - -
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Residues in contact with SER 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A VAL* 6.0 1.8 - - - -
20A GLU 4.5 3.5 + - - -
21A PRO 5.2 2.9 + - - -
22A VAL 3.4 0.6 - - - -
23A MET* 1.3 80.1 - - - +
25A GLN* 1.3 63.8 + - - +
27A VAL* 3.5 6.3 + - - +
28A GLU* 3.3 19.6 + - - +
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Residues in contact with GLN 25 (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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21A PRO 5.5 2.6 + - - +
22A VAL* 3.5 9.6 + - - +
24A SER* 1.3 78.0 - - - +
26A LEU* 1.3 60.6 + - - +
28A GLU* 3.4 15.9 + - - +
29A PHE* 2.9 53.3 + - + +
143A LEU* 3.4 31.8 - - + +
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Residues in contact with LEU 26 (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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13A ILE* 3.7 29.4 - - + -
22A VAL 2.8 19.6 + - - +
23A MET* 3.2 23.5 + - + +
25A GLN* 1.3 77.4 - - - +
27A VAL* 1.3 53.4 + - + +
29A PHE* 3.3 2.2 + - - +
30A TYR* 2.8 41.4 + - + +
50A PHE* 3.9 19.1 - - + -
53A LEU* 5.0 2.7 - - + -
140A ILE* 3.3 39.5 - - + -
143A LEU* 3.9 7.1 - - + +
144A LEU* 4.3 19.5 - - + -
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Residues in contact with VAL 27 (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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4A VAL* 3.7 37.9 - - + -
5A THR 3.6 17.5 - - - +
6A VAL* 3.9 17.5 - - + -
23A MET 3.0 17.1 + - - +
24A SER* 3.7 6.1 - - - +
26A LEU* 1.3 76.1 - - + +
28A GLU* 1.3 60.8 + - - +
30A TYR* 3.2 0.7 + - - -
31A ASN* 2.9 53.1 + - - +
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Residues in contact with GLU 28 (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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24A SER 3.3 11.1 + - - +
25A GLN* 3.4 19.7 + - - +
27A VAL* 1.3 80.8 - - - +
29A PHE* 1.3 78.8 + - - +
31A ASN* 4.0 5.3 - - - +
32A GLU* 3.4 35.7 + - + +
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Residues in contact with PHE 29 (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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25A GLN* 2.9 41.2 + - - +
26A LEU 3.7 1.1 - - - +
28A GLU* 1.3 91.3 - - - +
30A TYR* 1.3 62.0 + - - +
32A GLU* 3.5 24.4 + - - +
33A VAL* 3.5 25.1 - - - +
139A LYS* 3.7 54.3 - - + -
140A ILE* 3.6 21.7 - - + +
143A LEU* 4.6 13.9 - - + -
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Residues in contact with TYR 30 (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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6A VAL* 4.3 19.7 - - + -
8A HIS* 4.1 8.7 - - + -
9A ALA 2.7 28.4 + - - -
10A PRO* 3.7 5.5 - - + +
26A LEU* 2.8 28.4 + - + +
27A VAL* 3.9 3.6 - - - +
29A PHE* 1.3 71.5 - - - +
31A ASN* 1.3 62.6 + - - +
33A VAL* 5.1 2.2 - - + -
34A ALA* 2.8 58.0 + - + +
37A LEU* 4.7 10.2 - - + +
38A LEU* 4.5 4.0 - - - +
49A PHE* 3.5 21.3 - + - -
50A PHE* 3.6 32.1 - + - -
137A TRP* 3.8 23.3 - + - -
140A ILE* 3.9 10.5 - - + -
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Residues in contact with ASN 31 (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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6A VAL* 3.5 11.9 - - - +
7A SER* 2.9 47.1 + - - +
8A HIS* 4.0 23.8 + - - -
27A VAL* 2.9 36.9 + - - +
28A GLU* 4.0 5.7 - - - +
30A TYR* 1.3 77.7 - - - +
32A GLU* 1.3 63.2 + - - +
33A VAL 3.3 0.5 + - - -
34A ALA 4.1 1.9 + - - -
35A SER* 5.0 1.6 + - - -
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Residues in contact with GLU 32 (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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28A GLU* 3.4 23.3 + - + +
29A PHE* 3.5 34.7 - - - +
30A TYR 3.3 0.6 - - - -
31A ASN* 1.3 76.8 - - - +
33A VAL* 1.3 65.3 + - + +
35A SER* 4.9 1.0 + - - -
36A TRP* 3.3 25.3 - - - -
139A LYS* 5.3 5.0 - - - +
135C ILE* 4.9 1.4 - - - +
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Residues in contact with VAL 33 (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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29A PHE 3.5 16.8 + - - +
30A TYR* 3.4 4.7 + - + +
32A GLU* 1.3 88.9 - - + +
34A ALA* 1.3 65.9 + - - +
35A SER 3.2 2.5 - - - -
36A TRP* 2.9 20.7 + - + +
37A LEU* 3.1 9.2 + - + -
135A ILE 5.7 0.2 - - - +
136A TYR* 3.2 59.9 - - + +
139A LYS* 6.4 1.8 - - + -
140A ILE* 5.7 1.6 - - + -
135C ILE* 3.6 19.7 - - + -
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Residues in contact with ALA 34 (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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8A HIS* 3.7 25.8 - - + +
30A TYR* 2.8 51.4 + - + +
31A ASN* 4.1 0.8 + - - -
32A GLU 3.9 0.8 - - - -
33A VAL* 1.3 76.7 - - - +
35A SER* 1.3 56.6 + - - +
37A LEU* 3.2 7.5 + - - +
38A LEU* 2.8 40.0 + - + +
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Residues in contact with SER 35 (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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8A HIS* 3.9 29.4 + - - -
31A ASN 5.0 1.7 + - - -
32A GLU 4.9 1.0 + - - -
33A VAL 3.2 0.5 - - - -
34A ALA* 1.3 78.2 - - - +
36A TRP* 1.3 83.6 + - - +
38A LEU* 4.8 4.1 - - - +
39A ARG* 4.2 12.0 + - - +
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Residues in contact with TRP 36 (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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32A GLU 3.3 25.6 - - - -
33A VAL* 2.9 10.8 + - - +
35A SER* 1.3 98.1 + - - +
37A LEU* 1.3 65.4 + - - +
39A ARG* 3.5 18.5 - - - +
40A ASP* 5.0 2.3 - - - +
136A TYR* 3.7 27.4 + - + -
39C ARG* 5.0 3.3 + - - -
131C LYS 3.6 19.1 - - - -
132C SER* 2.6 34.8 + - - +
134C ALA* 4.3 15.3 - - + -
135C ILE* 3.8 23.4 - - + +
136C TYR* 3.4 24.8 - + - -
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Residues in contact with LEU 37 (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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30A TYR* 4.7 10.3 - - + +
33A VAL* 3.1 11.9 + - + +
34A ALA* 3.2 8.0 + - - +
36A TRP* 1.3 82.2 - - - +
38A LEU* 1.3 65.1 + - + +
39A ARG 3.2 5.0 + - - -
40A ASP* 3.6 11.3 + - - +
42A THR* 4.4 4.7 - - + +
49A PHE* 3.7 34.5 - - + -
124A SER* 4.1 7.2 - - - +
133A HIS* 4.0 19.5 + - + -
136A TYR* 3.8 32.5 - - + -
137A TRP* 3.5 38.8 - - + +
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Residues in contact with LEU 38 (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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8A HIS* 3.6 31.6 - - + -
9A ALA* 3.7 29.4 - - + +
30A TYR* 4.5 3.4 - - - +
34A ALA* 2.8 26.2 + - + +
35A SER* 4.3 4.0 + - - +
37A LEU* 1.3 72.1 - - + +
39A ARG* 1.3 64.7 + - - +
40A ASP 3.2 11.8 + - - +
42A THR* 5.8 0.7 - - + -
46A PRO* 3.7 31.0 - - + -
49A PHE* 4.5 9.4 - - + -
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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
------------------------------------------------------------
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