Contacts of the helix formed by residues 29 - 43 (chain A) in PDB entry 1T2E
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 GLY 29 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A GLY 3.5 3.4 + - - -
28A SER* 1.3 75.4 - - - +
30A MET* 1.3 61.8 + - - -
31A ILE 3.4 2.9 - - - -
32A GLY 3.8 3.0 - - - +
33A GLY 2.9 21.5 + - - -
58A MET* 4.7 1.6 - - - -
62A LYS* 3.0 18.0 + - - -
97A THR* 4.9 0.4 + - - -
336A NAI 3.3 31.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A GLY* 1.3 73.3 - - - -
31A ILE* 1.3 64.5 + - - +
33A GLY* 3.3 1.6 + - - -
35A VAL* 3.3 26.7 + - - +
62A LYS* 4.6 8.7 - - - +
245A ALA* 5.4 4.9 - - + -
247A TYR* 3.1 66.3 - - + +
336A NAI 2.9 26.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A MET* 1.3 73.9 - - - +
32A GLY* 1.3 68.1 + - - +
35A VAL* 3.1 3.8 + - - +
36A MET* 2.8 34.6 + - + +
97A THR* 3.8 6.7 - - + -
138A VAL* 4.2 5.4 - - + -
246A PRO 4.4 1.1 - - - +
247A TYR* 3.5 27.6 - - + +
250A PRO* 3.7 7.9 - - + -
251A ALA* 4.0 7.0 - - - -
254A ILE* 3.5 27.6 - - + -
336A NAI 2.9 71.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU* 3.5 8.6 - - - +
27A GLY 3.8 18.8 - - - -
28A SER* 4.4 1.1 - - - -
29A GLY 3.4 8.8 + - - +
30A MET 3.3 0.6 - - - -
31A ILE* 1.3 79.7 - - - +
33A GLY* 1.3 56.9 + - - +
36A MET* 3.3 17.4 + - - +
37A ALA* 2.9 26.9 + - - +
51A LEU* 3.7 8.0 - - - +
97A THR* 4.4 3.0 + - - -
336A NAI 4.3 0.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A GLY 2.9 17.0 + - - -
30A MET* 3.3 2.0 + - - -
31A ILE 3.1 0.4 - - - -
32A GLY* 1.3 77.9 - - - +
35A VAL* 1.3 62.4 + - - +
37A ALA* 3.4 6.2 + - - +
38A THR* 3.0 24.9 + - - -
51A LEU* 4.5 3.7 - - - +
62A LYS* 4.7 16.2 - - - -
66A THR* 5.0 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A MET 3.3 13.9 + - - +
31A ILE 3.1 2.7 + - - +
33A GLY* 1.3 77.2 - - - +
36A MET* 1.3 64.1 + - - +
38A THR* 3.2 9.5 + - + -
39A LEU* 2.9 37.2 + - + +
247A TYR* 3.5 29.2 - - + +
248A VAL* 4.4 21.1 - - + +
251A ALA* 3.4 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU* 4.1 18.4 - - + -
31A ILE* 2.8 23.5 + - + +
32A GLY* 3.5 25.6 - - - +
35A VAL* 1.3 77.1 - - - +
37A ALA* 1.3 63.3 + - - +
39A LEU* 3.1 1.7 + - - +
40A ILE* 2.8 29.4 + - - +
95A ILE* 3.5 39.7 - - + +
97A THR* 3.8 8.7 - - + +
251A ALA* 3.7 19.7 - - + +
254A ILE* 3.6 22.0 - - - -
255A ILE* 3.8 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU* 3.7 12.4 - - + +
32A GLY 2.9 17.4 + - - +
33A GLY* 3.8 4.5 - - - +
35A VAL 3.3 0.2 - - - -
36A MET* 1.3 76.4 - - - +
38A THR* 1.3 62.7 + - - +
40A ILE* 3.3 6.5 + - - +
41A VAL* 3.2 27.7 + - - +
49A VAL* 4.1 9.7 - - + +
51A LEU* 3.8 26.7 - - + -
66A THR* 3.9 13.7 - - + +
78A VAL* 4.7 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A GLY 3.0 14.8 + - - -
35A VAL* 3.3 14.7 - - + -
37A ALA* 1.3 77.7 - - - +
39A LEU* 1.3 64.8 + - + +
41A VAL* 3.3 3.9 + - - +
42A GLN* 2.9 44.9 + - + +
66A THR* 3.9 17.6 + - + +
69A THR* 5.1 8.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A VAL* 2.9 33.8 + - + +
36A MET 3.8 2.5 - - - +
38A THR* 1.3 80.1 - - + +
40A ILE* 1.3 62.0 + - - +
42A GLN* 3.2 15.8 + - + +
43A LYS* 2.9 46.7 + - - +
248A VAL* 5.2 0.7 - - + +
251A ALA 4.1 0.7 - - - -
252A ALA* 3.7 38.6 - - + +
255A ILE* 3.9 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ILE* 3.9 31.4 - - + -
25A LEU* 4.1 11.2 - - + -
36A MET 2.8 24.4 + - - +
37A ALA 3.7 4.5 - - - +
38A THR 3.2 0.2 - - - -
39A LEU* 1.3 78.5 - - - +
41A VAL* 1.3 56.9 + - - +
43A LYS 3.3 0.7 + - - -
44A ASN* 2.8 23.0 + - - -
45A LEU* 2.9 28.2 + - + -
46A GLY 3.4 24.5 - - - +
49A VAL* 3.3 32.5 - - + -
76A CYS* 4.2 0.4 - - + -
95A ILE* 5.0 0.2 - - + -
255A ILE* 3.7 23.1 - - + -
258A ALA* 6.4 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ALA 3.2 12.3 + - - +
38A THR 3.7 6.7 - - - +
40A ILE* 1.3 78.6 - - + +
42A GLN* 1.3 61.9 + - - +
44A ASN 2.9 4.6 + - - +
49A VAL* 5.2 0.7 - - + -
66A THR* 4.1 7.2 - - + +
69A THR* 3.4 24.9 - - - +
70A ASN* 3.6 35.2 - - - +
73A ALA* 4.3 1.8 - - + -
74A SER* 2.7 30.4 + - - -
76A CYS* 4.2 14.4 - - + -
78A VAL* 3.4 33.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A THR* 2.9 34.5 + - + +
39A LEU* 3.5 19.3 - - + +
41A VAL* 1.3 77.2 - - - +
43A LYS* 1.3 63.8 + - + +
44A ASN* 3.3 0.6 + - - +
69A THR* 4.5 16.2 + - - +
72A MET* 5.6 3.4 - - - +
73A ALA* 4.0 28.2 - - - +
74A SER* 4.2 4.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LEU* 2.9 32.6 + - - +
42A GLN* 1.3 81.2 - - + +
44A ASN* 1.3 71.5 + - - +
45A LEU* 3.2 24.1 + - + +
255A ILE* 3.8 26.7 - - + -
256A GLU* 6.4 0.4 - - - +
259A GLU* 4.1 24.3 + - - +
263A LYS* 4.5 8.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A LYS* 5.9 5.1 - - - +
40A ILE 2.8 8.7 + - - -
41A VAL 2.9 6.8 + - - -
42A GLN 3.3 0.4 - - - +
43A LYS* 1.3 80.7 - - - +
45A LEU* 1.3 61.6 + - - +
46A GLY* 3.4 3.3 + - - -
73A TYR 5.4 0.7 - - - +
74A SER* 3.4 14.3 - - - +
75A ASN* 2.9 34.0 + - - +
76A CYS* 3.1 17.0 - - - -
----------------------------------------------------------
Back to top of page
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