Contacts of the helix formed by residues 31 - 49 (chain A) in PDB entry 3HW4
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 GLU 31 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A MET* 3.4 22.7 - - + +
26A GLU* 5.0 8.1 - - + -
27A ASP 2.9 13.7 + - - +
28A PRO 4.1 0.7 - - - -
30A ILE* 1.3 83.0 - - + +
32A THR* 1.3 59.6 + - - +
33A ASN* 3.5 5.3 + - - +
34A LYS* 2.8 38.9 + - + +
35A PHE* 3.0 22.2 + - - +
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Residues in contact with THR 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 3.4 33.1 - - - +
2A GLU* 4.2 18.2 - - + +
28A PRO 3.2 20.9 - - - +
29A LYS 3.4 21.8 - - - +
30A ILE 2.9 7.6 + - - +
31A GLU* 1.3 71.1 + - - +
33A ASN* 1.4 65.0 + - - +
35A PHE* 3.2 5.3 + - - +
36A ALA 3.0 23.7 + - - -
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Residues in contact with ASN 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 3.6 20.0 - - - +
31A GLU* 3.5 2.8 + - - +
32A THR* 1.4 79.2 + - - +
34A LYS* 1.3 66.0 + - - +
36A ALA 3.4 1.4 + - - +
37A ALA* 3.0 19.3 + - - +
124A ARG* 4.7 3.4 - - - +
187A LEU 4.7 0.7 - - - +
190A SER* 2.8 28.6 + - - -
191A PHE* 3.2 34.5 + - + -
194A SER* 3.2 31.3 + - - +
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Residues in contact with LYS 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A MET* 4.0 7.0 - - + -
26A GLU* 3.5 32.8 + - - +
31A GLU* 2.8 47.3 + - + +
32A THR 3.3 0.2 - - - -
33A ASN* 1.3 78.7 - - - +
35A PHE* 1.3 56.1 + - - +
37A ALA* 3.2 7.8 + - + +
38A ILE* 2.8 52.1 + - + +
124A ARG* 5.7 0.9 - - - +
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Residues in contact with PHE 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A GLU* 4.3 18.6 - - + -
5A VAL* 3.3 40.4 - - + -
6A ARG* 4.1 7.9 - - - -
14A VAL* 3.7 24.7 - - + -
17A ALA* 4.1 6.1 - - + -
18A GLU* 3.8 26.2 - - + -
21A MET* 3.5 24.7 - - - -
28A PRO* 3.5 27.4 - - + +
31A GLU 3.0 15.1 + - - +
32A THR* 3.2 12.3 + - - +
34A LYS* 1.3 74.3 - - - +
36A ALA* 1.3 57.1 + - - +
38A ILE* 3.6 2.5 + - - +
39A CYS* 3.1 30.2 + - - -
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Residues in contact with ALA 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 3.7 21.1 - - + -
5A VAL* 3.8 15.1 - - + +
9A PHE* 4.1 3.6 - - + -
32A THR 3.0 7.8 + - - +
33A ASN 3.8 1.6 - - - +
34A LYS 3.3 0.2 - - - -
35A PHE* 1.3 73.5 - - - +
37A ALA* 1.3 58.9 + - - +
39A CYS* 3.4 4.3 + - - +
40A THR* 3.0 33.8 + - - -
182A MET* 3.7 28.9 - - + -
191A PHE* 3.8 8.7 - - + -
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Residues in contact with ALA 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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33A ASN 3.0 12.0 + - - +
34A LYS* 3.5 12.3 - - + +
36A ALA* 1.3 73.6 - - - +
38A ILE* 1.3 59.7 + - + +
40A THR* 3.4 5.5 + - - -
41A HIS* 2.9 30.3 + - - +
122A VAL* 5.7 2.3 - - - +
124A ARG* 3.3 30.7 - - - +
191A PHE* 3.6 12.0 - - + -
257A TMP 5.1 2.9 - - - +
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Residues in contact with ILE 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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17A ALA* 3.5 29.8 - - + +
20A ALA* 4.6 0.4 - - + -
21A MET* 3.7 27.8 - - + +
26A GLU* 4.6 5.4 - - - +
34A LYS* 2.8 36.2 + - + +
35A PHE* 3.8 4.3 - - - +
37A ALA* 1.3 75.9 - - + +
39A CYS* 1.3 59.0 + - - +
41A HIS 3.4 0.2 + - - -
42A LEU* 2.9 11.3 + - - +
257A TMP 2.9 86.8 - - + +
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Residues in contact with CYS 39 (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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5A VAL* 3.7 26.0 - - - -
9A PHE* 3.8 24.5 - - + -
13A ILE* 3.4 17.4 - - + +
14A VAL* 4.0 14.8 - - - -
17A ALA* 3.5 21.3 - - - -
35A PHE* 3.1 25.2 + - - +
36A ALA 3.7 6.7 - - - +
38A ILE* 1.3 76.7 - - - +
40A THR* 1.3 58.9 + - - +
42A LEU* 3.3 0.6 + - - -
43A GLU* 2.8 27.5 + - - +
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Residues in contact with THR 40 (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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9A PHE* 3.3 21.9 - - - -
36A ALA 3.0 23.5 + - - -
37A ALA* 3.6 7.6 - - - -
38A ILE 3.3 0.2 - - - -
39A CYS* 1.3 73.1 - - - +
41A HIS* 1.3 62.6 + - - +
43A GLU* 3.3 2.9 + - - +
44A VAL* 2.8 28.3 + - + +
122A VAL* 3.9 10.3 - - + -
150A PHE* 3.7 18.0 - - + -
175A LEU* 3.4 32.1 - - + -
178A ILE* 3.8 14.9 - - + +
182A MET* 5.1 0.2 - - - +
191A PHE* 4.8 1.4 - - - -
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Residues in contact with HIS 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ALA 2.9 16.6 + - - +
39A CYS 3.3 0.2 - - - -
40A THR* 1.3 75.6 - - - +
42A LEU* 1.3 64.5 + - - +
44A VAL* 3.2 2.6 + - - +
45A CYS* 2.9 36.6 + - - -
80A GLU* 3.2 25.4 - - + -
108A ASP* 3.1 17.0 + - - -
120A ILE* 2.9 34.4 + - + -
122A VAL* 4.0 24.0 - - + +
130A TYR* 5.8 0.2 - - - -
257A TMP 2.6 53.8 + - + +
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Residues in contact with LEU 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ILE* 3.7 13.9 - - + +
16A LEU* 3.7 9.6 - - + -
17A ALA* 3.5 41.3 - - + +
38A ILE 2.9 18.8 + - - +
39A CYS* 3.5 4.7 - - - +
41A HIS* 1.3 76.8 - - - +
43A GLU* 1.3 62.1 + - - +
45A CYS* 3.0 7.8 + - + +
46A PHE* 3.0 44.7 + - + -
80A GLU* 3.7 12.8 - - + +
81A GLY* 3.7 24.5 - - - -
257A TMP 3.2 26.8 - - + +
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Residues in contact with GLU 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A PHE* 3.1 16.7 - - + -
10A ASN* 5.2 1.2 + - - -
13A ILE* 3.8 26.7 - - + +
39A CYS 2.8 19.5 + - - +
40A THR* 3.7 6.1 - - - +
42A LEU* 1.3 73.4 - - - +
44A VAL* 1.3 63.1 + - + +
46A PHE* 3.2 5.2 + - + +
47A MET* 3.0 38.9 + - + +
174A ARG* 2.9 50.6 + - + +
178A ILE* 5.3 1.1 - - + -
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Residues in contact with VAL 44 (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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40A THR* 2.8 21.6 + - + +
41A HIS 3.2 4.0 + - - +
43A GLU* 1.3 74.6 - - + +
45A CYS* 1.3 63.4 + - - +
47A MET* 3.2 21.4 + - + +
48A TYR* 2.9 23.6 + - + +
120A ILE* 3.8 21.5 - - + -
122A VAL* 3.6 18.8 - - + -
148A PHE* 4.1 13.2 - - + -
171A ILE* 3.8 24.7 - - + -
175A LEU* 4.0 19.1 - - + -
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Residues in contact with CYS 45 (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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41A HIS* 2.9 46.2 + - - -
42A LEU* 3.0 11.0 + - + +
44A VAL* 1.3 76.5 - - - +
46A PHE* 1.3 58.7 + - + +
48A TYR* 3.5 6.8 + - - +
49A SER* 2.9 26.4 + - - -
78A ILE* 3.9 20.0 - - + -
80A GLU* 4.1 7.2 - - + -
108A ASP* 3.8 21.8 - - - -
109A LEU* 4.0 6.5 - - + +
120A ILE* 4.0 13.7 - - - -
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Residues in contact with PHE 46 (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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12A MET* 5.4 10.1 - - - -
13A ILE* 4.2 19.5 - - + -
16A LEU* 3.8 31.4 - - + -
42A LEU* 3.0 40.2 + - + -
43A GLU* 3.2 6.5 + - + +
45A CYS* 1.3 71.8 - - - +
47A MET* 1.3 65.2 + - + +
49A SER* 3.3 7.7 + - - -
50A ASP 2.9 33.3 + - - +
78A ILE* 4.0 34.8 - - + -
80A GLU 4.8 5.2 - - - -
81A GLY* 5.5 0.2 - - - -
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Residues in contact with MET 47 (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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43A GLU* 3.0 24.4 + - + +
44A VAL* 3.2 39.7 + - + +
46A PHE* 1.3 73.2 - - + +
48A TYR* 1.3 65.8 + - - +
50A ASP* 3.1 14.4 + - - +
167A SER* 5.2 4.5 + - - -
170A ARG* 4.5 7.7 + - - +
171A ILE* 3.7 39.1 - - + +
174A ARG* 3.9 34.5 - - + -
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Residues in contact with TYR 48 (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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44A VAL* 2.9 15.8 + - + +
45A CYS* 3.6 7.2 - - - +
46A PHE 3.4 0.2 - - - -
47A MET* 1.3 77.5 - - - +
49A SER* 1.3 60.1 - - - +
50A ASP* 3.7 0.5 + - - +
76A PHE* 3.6 34.0 - + - -
109A LEU* 3.4 27.1 - - + -
118A ILE* 4.1 12.0 - - + +
120A ILE* 3.7 20.9 - - + -
144A HIS* 5.6 1.0 - - - -
146A HIS* 2.9 39.5 + + - +
148A PHE* 3.9 17.5 - + - -
162A THR* 3.5 19.9 + - + -
163A LEU* 3.7 39.0 - - + +
171A ILE* 4.1 6.0 - - + +
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Residues in contact with SER 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A CYS 2.9 16.4 + - - -
46A PHE* 3.3 12.8 + - - -
47A MET 3.1 0.2 - - - -
48A TYR* 1.3 80.4 - - - +
50A ASP* 1.3 69.2 + - - +
76A PHE* 3.6 40.3 + - - +
78A ILE* 4.5 9.1 - - - +
109A LEU* 4.1 12.9 - - - +
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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) + - + + + + + -
------------------------------------------------------------
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