Contacts of the helix formed by residues 31 - 50 (chain A) in PDB entry 4TXQ
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 ASP 31 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A HIS* 2.8 28.5 + - + +
30A ARG* 1.3 81.5 - - + +
32A PRO* 1.3 67.4 - - - +
33A VAL* 3.3 14.4 + - - +
34A VAL* 3.1 23.6 + - + +
35A ALA 3.0 17.2 + - - -
89A HIS* 2.7 38.0 + - - -
93A TYR* 5.1 6.6 - - + -
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Residues in contact with PRO 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A HIS 3.5 2.0 - - - +
28A ASP 3.8 15.7 - - - +
29A LYS 3.8 9.9 - - - +
30A ARG 3.9 1.6 - - - +
31A ASP* 1.3 89.8 - - - +
33A VAL* 1.3 57.0 + - + +
35A ALA* 3.6 10.3 - - + +
36A TYR* 2.8 30.1 + - - +
70A LEU* 4.0 16.5 - - + +
73A GLN* 4.3 13.0 - - - +
74A LEU* 3.8 25.0 - - + +
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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
----------------------------------------------------------
31A ASP* 3.1 11.9 + - - +
32A PRO* 1.3 75.4 - - + +
34A VAL* 1.3 63.5 + - - +
36A TYR* 3.3 5.1 + - - +
37A TYR* 3.0 44.4 + - + -
74A LEU* 4.5 9.9 - - + -
77A ASN* 3.7 28.0 - - - +
79A ALA* 3.8 24.0 - - + -
80A ILE* 4.5 4.7 - - + -
89A HIS* 3.5 27.1 - - + +
90A LEU* 4.3 1.6 - - + -
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Residues in contact with VAL 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A HIS* 3.9 25.1 - - + +
31A ASP* 3.1 33.4 + - + +
33A VAL* 1.3 76.4 - - - +
35A ALA* 1.3 57.9 + - - +
37A TYR* 3.4 1.0 + - - +
38A CYS* 2.9 44.6 + - - -
89A HIS* 4.0 13.9 - - + +
90A LEU* 4.1 14.8 - - + +
93A TYR* 4.0 19.1 - - + -
124A LEU* 4.0 16.6 - - + -
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Residues in contact with ALA 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ALA* 3.3 25.1 - - - +
27A HIS* 3.9 1.5 - - - +
28A ASP* 3.2 35.4 - - - +
31A ASP 3.0 12.8 + - - +
32A PRO* 3.7 9.6 - - + +
34A VAL* 1.3 78.1 - - - +
36A TYR* 1.3 62.2 - - - +
39A ARG* 3.1 32.8 + - - +
70A LEU* 4.3 2.0 - - + -
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Residues in contact with TYR 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A PRO 2.8 18.6 + - - +
33A VAL* 3.5 4.0 - - - +
35A ALA* 1.3 76.9 - - - +
37A TYR* 1.3 82.4 + + - +
39A ARG* 3.2 3.0 + - - -
40A LEU* 2.9 34.4 + - + +
67A LEU* 3.5 46.0 - - + +
70A LEU* 3.6 20.6 - - + +
71A LYS* 4.0 16.2 - - + +
74A LEU* 4.0 9.6 - - + -
80A ILE* 3.7 31.9 - - + +
195C LEU* 3.3 34.3 + - + +
196C ARG* 5.0 2.9 - - - +
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Residues in contact with TYR 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A VAL* 3.0 37.3 + - + +
34A VAL 4.3 0.4 - - - +
36A TYR* 1.3 87.8 - + - +
38A CYS* 1.3 61.3 + - - +
40A LEU* 3.6 24.6 - - + +
41A TYR 2.9 24.9 + - - -
79A ALA 2.5 30.0 + - - -
80A ILE* 3.5 30.0 + - + +
83A GLU* 4.5 8.0 - - + +
86A GLY* 3.9 8.9 - - - -
90A LEU* 3.9 18.6 - - + -
127A VAL* 3.3 22.9 - - + +
130A VAL* 4.1 4.2 - - + +
131A PHE* 3.5 32.2 - + + -
196C ARG* 5.6 1.8 - - - -
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Residues in contact with CYS 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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20A HIS* 3.5 25.0 - - - +
23A THR* 3.9 28.7 - - - -
24A ALA* 3.7 12.1 - - + -
34A VAL* 2.9 34.6 + - - +
37A TYR* 1.3 77.1 - - - +
39A ARG* 1.3 61.1 + - - +
41A TYR* 3.5 3.5 + - - +
42A ALA* 3.1 21.8 + - - +
90A LEU* 5.7 0.2 - - - -
123A LEU* 6.5 0.4 - - - -
124A LEU* 4.3 5.8 - - - -
127A VAL* 3.9 24.5 - - + -
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Residues in contact with ARG 39 (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 13.4 - - - +
5A ALA 5.3 2.4 + - - +
7A LEU* 5.7 0.2 - - - +
21A LEU* 4.5 6.0 - - + +
24A ALA* 3.9 14.8 - - + +
25A GLN* 4.1 16.0 - - - +
28A ASP* 2.7 43.6 + - - -
35A ALA* 3.1 23.2 + - - +
36A TYR 3.6 3.4 - - - +
38A CYS* 1.3 77.0 - - - +
40A LEU* 1.3 58.6 + - - +
42A ALA* 3.2 7.3 + - - +
43A MET* 2.8 30.7 + - - +
63A LEU* 3.8 21.3 - - + +
66A GLN* 2.9 43.6 + - - +
67A LEU* 3.5 20.1 - - + +
70A LEU* 3.9 10.8 - - - +
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Residues in contact with LEU 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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36A TYR* 2.9 23.4 + - + +
37A TYR* 3.2 34.1 + - + +
39A ARG* 1.3 75.6 - - - +
41A TYR* 1.3 64.7 + - - +
43A MET* 3.3 2.4 + - - +
44A GLN* 2.9 33.8 + - - +
67A LEU* 3.6 10.5 - - + +
130A VAL* 4.3 7.0 - - + -
192C LEU* 3.7 29.8 - - + -
195C LEU* 4.0 17.7 - - + -
196C ARG* 3.6 39.0 - - + +
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Residues in contact with TYR 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A SER 5.6 0.2 + - - -
17A ILE* 4.4 7.1 - - + +
20A HIS* 3.4 48.3 + + + -
37A TYR 2.9 15.8 + - - +
38A CYS 3.7 3.4 - - - +
40A LEU* 1.3 77.6 - - - +
42A ALA* 1.3 57.5 + - - +
44A GLN* 3.8 2.1 - - + +
45A THR* 2.7 62.3 + - - +
48A LYS* 6.0 2.0 - - - -
126A ASP* 3.3 39.1 - - + +
127A VAL* 3.8 15.7 - - + -
129A THR* 3.4 15.5 - - + -
130A VAL* 3.6 17.6 - - + +
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Residues in contact with ALA 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ILE* 3.5 37.3 - - + +
20A HIS* 4.9 3.1 - - + -
21A LEU* 3.6 32.3 - - + -
38A CYS 3.1 12.3 + - - +
39A ARG 3.2 7.4 + - - +
41A TYR* 1.3 74.3 - - - +
43A MET* 1.3 60.2 + - - +
46A GLY* 2.9 24.9 + - - -
60A LEU* 4.8 0.7 - - - +
63A LEU* 4.0 5.5 - - + +
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Residues in contact with MET 43 (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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39A ARG 2.8 16.8 + - - +
40A LEU* 3.5 6.1 - - + +
42A ALA* 1.3 76.3 - - - +
44A GLN* 1.3 58.5 + - - +
46A GLY* 3.1 2.8 + - - -
47A MET* 3.0 63.5 + - + +
60A LEU* 3.2 48.3 - - + +
63A LEU* 3.5 17.1 - - + +
64A MET* 3.6 32.1 - - + -
67A LEU* 3.7 16.4 - - + -
188C LEU* 4.2 9.9 - - + -
192C LEU* 4.6 5.2 - - + -
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Residues in contact with GLN 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 LEU* 2.9 28.7 + - + +
41A TYR* 3.9 5.2 - - + +
43A MET* 1.3 78.7 - - + +
45A THR* 1.3 61.7 + - - +
47A MET* 3.7 10.5 + - - +
48A LYS* 3.5 35.9 + - + +
129A THR 5.7 0.4 + - - -
130A VAL* 4.0 14.7 + - + +
192C LEU* 4.7 16.3 - - + +
196C ARG* 2.9 33.4 + - - +
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Residues in contact with THR 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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16A SER* 4.8 3.4 - - - +
17A ILE* 3.7 25.8 - - + -
41A TYR* 2.7 51.5 + - - +
44A GLN* 1.3 75.4 - - - +
46A GLY* 1.3 63.0 + - - +
48A LYS* 3.4 19.2 + - - +
49A ILE* 3.1 38.0 + - + +
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Residues in contact with GLY 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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14A PHE* 3.5 31.2 - - - -
17A ILE* 4.8 3.1 - - - +
42A ALA 2.9 18.5 + - - -
43A MET 3.6 1.3 - - - -
45A THR* 1.3 77.2 - - - +
47A MET* 1.3 61.5 + - - +
49A ILE* 3.3 1.8 + - - -
50A ASP 3.1 27.7 + - - +
60A LEU* 4.0 7.0 - - - -
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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 MET* 3.0 52.7 + - + +
44A GLN* 3.8 8.1 - - - +
46A GLY* 1.3 78.0 - - - +
48A LYS* 1.3 62.4 + - + +
50A ASP* 4.2 0.2 - - - -
51A SER* 3.3 36.4 + - - -
60A LEU* 4.0 13.6 - - + +
188C LEU* 3.9 19.5 - - + +
189C SER* 5.0 10.3 - - - -
192C LEU* 3.6 44.6 - - + -
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Residues in contact with LYS 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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41A TYR* 6.0 1.8 - - - -
44A GLN* 3.5 25.4 + - + +
45A THR* 3.4 22.0 + - - +
46A GLY 3.4 0.6 - - - -
47A MET* 1.3 80.0 - - + +
49A ILE* 1.3 65.0 + - + +
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Residues in contact with ILE 49 (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 GLN* 3.7 31.6 - - + +
14A PHE* 4.1 15.7 - - + -
16A SER* 3.9 19.3 - - - +
17A ILE* 5.5 1.3 - - + -
45A THR* 3.1 31.8 + - + +
46A GLY* 3.7 4.3 - - - +
47A MET 3.3 0.2 - - - -
48A LYS* 1.3 82.0 - - + +
50A ASP* 1.3 67.3 + - + +
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Residues in contact with ASP 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A GLN* 2.8 28.3 - - - +
14A PHE* 3.5 3.8 - - + -
46A GLY 3.1 12.4 + - - +
47A MET 4.2 0.2 - - - -
48A LYS 3.6 0.8 - - - -
49A ILE* 1.3 89.8 - - + +
51A SER* 1.3 58.6 + - - +
52A LYS* 3.0 4.9 + - - +
53A THR* 2.8 47.0 + - - -
56A CYS* 3.4 22.6 - - - +
60A LEU* 4.0 1.4 - - - +
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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
------------------------------------------------------------
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