Contacts of the helix formed by residues 60 - 74 (chain A) in PDB entry 1TW2
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 ARG 60 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A ALA* 4.4 0.7 - - - -
59A THR* 1.3 73.7 - - - +
61A PRO* 1.3 68.1 - - + +
62A GLU* 4.6 2.2 - - + +
63A ALA* 3.3 12.2 + - + +
64A LEU* 2.9 27.9 + - - +
126B ILE 3.2 7.2 + - - +
127B ARG 3.3 26.8 + - - +
128B THR* 3.3 37.7 + - - +
129B GLY* 4.0 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A VAL* 3.7 16.5 - - + +
51A LYS* 5.1 13.0 - - + -
54A ALA* 3.8 21.8 - - + -
59A THR 3.5 7.6 - - - +
60A ARG* 1.3 86.9 - - + +
62A GLU* 1.3 61.9 + - - +
64A LEU* 3.6 1.5 + - + -
65A LEU* 3.1 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ARG* 3.3 2.5 - - + +
61A PRO* 1.3 77.7 - - - +
63A ALA* 1.3 61.7 + - - +
65A LEU* 3.2 19.7 + - - +
66A ARG* 3.2 37.5 + - - +
69A ARG* 3.9 19.6 + - - -
316B LYS* 3.6 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ARG* 3.3 12.3 + - + +
62A GLU* 1.3 74.3 - - - +
64A LEU* 1.3 61.1 + - - +
66A ARG* 3.2 14.5 + - - +
67A LEU 3.0 22.2 + - - -
125B ALA 4.0 7.9 - - - +
126B ILE* 3.3 43.8 - - + +
129B GLY* 4.6 7.4 - - - -
304B LEU* 4.8 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A LEU* 4.7 0.7 - - + -
39A LEU* 3.8 27.1 - - + -
50A VAL* 3.8 13.5 - - + +
53A LEU* 3.7 21.8 - - + -
54A ALA* 3.6 32.3 - - - +
57A THR* 4.4 1.8 - - - +
59A THR* 3.7 15.9 - - + +
60A ARG 2.9 17.3 + - - +
61A PRO* 3.8 4.9 - - + +
63A ALA* 1.3 72.5 - - - +
65A LEU* 1.3 60.3 + - - +
67A LEU* 3.1 12.2 + - + +
68A ILE* 2.8 38.8 + - + +
126B ILE* 4.1 16.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A VAL* 4.1 28.9 - - + +
61A PRO 3.1 14.0 + - - +
62A GLU* 3.2 29.1 + - - +
64A LEU* 1.3 76.6 - - - +
66A ARG* 1.3 58.4 + - - +
68A ILE* 3.2 7.0 + - + +
69A ARG* 2.9 36.7 + - + +
85A PHE* 4.2 20.2 - - + -
288B HIS* 3.6 31.4 - - + +
292B PHE* 4.9 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A GLU* 3.2 34.3 + - - +
63A ALA* 3.2 13.8 + - - +
64A LEU 3.2 0.4 - - - -
65A LEU* 1.3 75.0 - - - +
67A LEU* 1.3 64.3 + - - +
69A ARG* 3.6 29.3 - - - +
70A HIS 3.7 3.3 + - - -
129B GLY 5.3 1.4 + - - -
297B THR* 4.7 1.2 - - - +
300B ASP* 2.9 56.4 + - - +
301B LEU* 3.9 24.5 - - + +
304B LEU* 3.5 33.8 - - + +
308B GLY 5.0 2.6 + - - -
309B GLY 3.0 25.7 + - - -
310B ALA* 3.8 12.9 - - - +
311B LEU 5.8 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A VAL* 4.0 24.0 - - + +
33A THR* 3.5 17.9 - - - +
34A ALA* 4.5 5.4 - - + +
37A LEU* 4.4 13.0 - - + -
39A LEU* 4.4 11.9 - - + -
63A ALA 3.0 12.2 + - - +
64A LEU* 3.5 14.8 - - + +
66A ARG* 1.3 77.0 - - - +
68A ILE* 1.3 60.6 + - - +
70A HIS* 3.2 9.1 + - - +
71A LEU* 3.2 38.2 + - + +
122B LEU* 3.3 34.1 - - + -
126B ILE* 3.8 10.1 - - + -
301B LEU* 4.5 4.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LEU* 4.7 4.5 - - + -
50A VAL* 4.4 20.6 - - + -
53A LEU* 4.1 20.6 - - + -
64A LEU* 2.8 39.5 + - + +
65A LEU* 3.2 7.2 + - + +
67A LEU* 1.3 73.4 - - - +
69A ARG* 1.3 67.0 + - - +
71A LEU* 4.0 12.1 - - + -
72A VAL* 2.9 20.3 + - + +
77A LEU* 3.6 23.6 - - + -
85A PHE* 3.6 40.2 - - + -
292B PHE* 4.7 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A GLU* 3.9 19.6 + - - -
65A LEU* 2.9 25.0 + - + +
66A ARG* 3.6 26.2 - - - +
67A LEU 3.2 0.4 - - - -
68A ILE* 1.3 77.7 - - - +
70A HIS* 1.3 61.7 + - - +
72A VAL* 3.3 4.9 + - - +
73A ALA* 3.2 19.4 + - - +
288B HIS* 3.1 31.8 + - - -
291B SER* 2.9 40.2 + - - +
292B PHE* 3.7 29.0 - - + -
296B PHE* 3.5 29.8 - - - -
297B THR* 3.6 13.9 - - + -
300B ASP* 4.6 2.0 + - - -
311B LEU 5.2 4.6 + - - -
313B THR* 4.3 10.9 - - - +
316B LYS* 5.5 3.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A HIS* 4.1 11.4 - + + +
27A THR* 3.1 44.7 + - + -
30A VAL* 3.3 23.8 - - + +
66A ARG 3.7 0.6 + - - -
67A LEU 3.2 8.8 + - - +
69A ARG* 1.3 80.1 - - - +
71A LEU* 1.3 59.3 + - - +
73A ALA* 3.1 19.2 + - + +
74A ILE* 3.1 32.9 + - + +
294B GLU* 4.7 10.2 - - - +
297B THR* 2.9 36.3 - - - -
298B GLU* 5.3 3.4 - - + +
301B LEU* 4.0 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A VAL* 3.5 23.6 - - + +
34A ALA* 3.8 20.9 - - + -
39A LEU* 3.4 32.5 - - + -
67A LEU* 3.2 28.2 + - + +
68A ILE* 3.7 7.0 - - - +
70A HIS* 1.3 74.3 - - - +
72A VAL* 1.3 60.3 + - - +
74A ILE* 4.1 4.3 - - + -
75A GLY 3.5 2.3 + - - -
76A LEU* 2.9 53.5 + - + +
77A LEU* 3.0 31.3 + - + -
94A LEU* 6.1 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ILE* 2.9 20.7 + - + +
69A ARG 3.5 8.1 - - - +
71A LEU* 1.3 77.7 - - - +
73A ALA* 1.3 62.2 + - - +
75A GLY* 3.4 10.7 + - - -
77A LEU 3.2 26.3 - - - +
78A GLU* 4.3 7.4 - - + +
79A GLU* 5.3 1.6 - - + +
85A PHE* 3.7 34.8 - - + -
292B PHE* 3.8 25.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ARG 3.2 10.5 + - - +
70A HIS* 3.1 13.4 + - + +
72A VAL* 1.3 76.0 - - - +
74A ILE* 1.3 61.6 + - + +
75A GLY 3.4 0.2 - - - -
292B PHE 3.6 21.3 - - - +
293B ASN* 3.6 23.3 - - - -
294B GLU* 3.9 19.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A THR* 3.8 30.1 - - + +
30A VAL* 4.7 4.5 - - + -
31A VAL* 4.0 21.1 - - + -
70A HIS* 3.3 46.9 - - + +
71A LEU* 3.9 11.4 - - - +
73A ALA* 1.3 78.8 - - + +
75A GLY* 1.3 58.9 + - - +
76A LEU* 3.9 14.3 - - + +
22B LEU* 3.5 33.5 - - + +
294B GLU* 4.7 11.7 - - + +
----------------------------------------------------------
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