Contacts of the helix formed by residues 19 - 30 (chain B) in PDB entry 3TQI
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 TYR 19 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B SER* 3.0 14.5 + - - +
18B GLN* 1.3 109.1 + - + +
20B ALA* 1.3 66.7 + - - +
21B GLN 3.1 10.7 - - - +
22B LEU* 3.7 23.5 - - + +
23B ILE* 3.2 19.7 + - - +
57B SER* 5.5 0.9 - - - -
108B PHE* 6.3 2.2 - + - -
140B TRP* 4.9 11.9 + - - -
181B HIS* 4.3 18.4 - + + -
183B GLU* 3.1 20.4 - - - +
184B VAL* 3.8 24.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 20 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ILE* 4.5 0.3 - - - +
14B ASP* 3.2 37.0 - - - +
16B GLY 4.0 3.1 - - - +
17B SER* 3.1 14.3 + - - +
18B GLN 3.3 1.4 - - - +
19B TYR* 1.3 78.7 - - - +
21B GLN* 1.3 62.7 + - + +
23B ILE* 3.1 24.6 + - - +
24B ALA 3.6 2.6 + - - -
36B LEU* 4.2 18.0 - - + +
57B SER* 4.1 13.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 21 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B GLN 3.6 7.5 + - - +
19B TYR* 3.1 9.4 - - - -
20B ALA* 1.3 79.8 + - + +
22B LEU* 1.3 68.9 + - - +
24B ALA* 4.4 6.3 - - - -
25B ARG* 5.1 2.5 - - + +
36B LEU* 3.4 21.4 - - + +
338B PRO* 4.4 17.0 + - - +
341B ILE* 3.7 37.2 - - + +
379B PHE* 4.1 18.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 22 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B TYR* 3.7 32.3 - - + +
21B GLN* 1.3 82.1 - - - +
23B ILE* 1.3 63.6 + - - +
24B ALA 3.6 4.2 - - - +
25B ARG* 3.5 49.2 - - + +
26B ARG* 2.9 59.5 + - - +
183B GLU* 4.0 25.1 - - + +
184B VAL* 4.8 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 23 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ILE* 3.9 11.4 - - + -
19B TYR 3.2 17.7 - - - +
20B ALA* 3.1 10.6 + - - +
22B LEU* 1.3 74.8 - - - +
24B ALA* 1.3 65.8 + - - +
26B ARG* 3.5 4.0 - - - +
27B VAL* 3.0 24.2 + - + +
55B ILE* 3.9 37.5 - - + -
57B SER* 3.9 24.2 - - - -
85B ILE* 3.2 34.1 - - + -
183B GLU* 3.5 18.3 - - + +
194B LEU* 4.7 6.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 24 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ILE* 3.4 22.9 - - + +
20B ALA 3.6 1.7 + - - +
21B GLN* 4.4 6.5 - - - -
22B LEU 3.6 5.3 - - - +
23B ILE* 1.3 78.8 - - - +
25B ARG* 1.3 63.1 + - - +
27B VAL 3.2 2.1 + - - -
28B ARG* 2.9 27.3 + - - +
34B CYS* 3.4 11.3 - - - +
36B LEU* 5.0 11.4 - - + +
337B TYR* 5.8 0.7 - - + -
379B PHE* 3.6 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 25 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B GLN* 4.9 2.3 - - - +
22B LEU* 3.4 47.7 + - + +
23B ILE 3.3 0.4 - - - -
24B ALA* 1.3 76.6 - - - +
26B ARG* 1.3 61.1 + - - +
28B ARG* 3.1 9.6 + - - +
29B GLU* 2.9 29.0 + - - +
379B PHE* 3.8 40.6 - - + -
380B LYS* 6.1 1.2 - - - +
381B ASP* 3.3 40.5 + - - +
384B ARG* 5.7 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 26 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B LEU* 2.9 46.5 + - - +
23B ILE 3.5 3.8 - - - +
25B ARG* 1.3 79.7 - - - +
27B VAL* 1.3 63.0 + - - +
29B GLU* 3.2 22.0 + - - +
30B ILE* 3.0 30.3 + - + +
182B PRO 4.9 0.8 + - - -
183B GLU* 2.9 31.6 + - - +
184B VAL* 4.5 1.0 - - - +
185B THR* 4.0 24.9 - - - +
191B HIS* 4.5 22.8 - - - +
194B LEU* 3.7 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 27 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ILE* 4.3 13.0 - - + -
12B ILE* 4.6 4.9 - - + -
23B ILE* 3.0 19.0 + - + +
24B ALA 3.5 7.4 - - - +
26B ARG* 1.3 76.3 - - + +
28B ARG* 1.3 61.6 + - - +
30B ILE* 3.3 18.7 + - + +
31B GLY 3.4 0.5 + - - -
32B VAL* 3.2 40.4 + - + +
34B CYS* 3.8 19.5 - - + -
55B ILE* 4.1 20.2 - - + -
194B LEU* 5.3 4.5 - - + -
198B VAL* 4.1 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 28 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ALA 2.9 22.6 + - - +
25B ARG* 3.4 8.3 - - - +
27B VAL* 1.3 75.4 - - - +
29B GLU* 1.3 64.5 + - - +
31B GLY* 3.0 15.4 + - - -
32B VAL 3.6 11.2 - - - -
33B TYR* 3.7 16.8 + - - -
34B CYS* 2.9 43.9 + - - +
208B TRP* 3.6 32.9 - - - +
337B TYR* 3.9 17.6 - - - -
377B GLU* 2.6 30.7 + - - +
379B PHE* 4.0 14.4 - - + -
382B GLU* 2.8 45.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 29 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ARG 2.9 13.1 + - - +
26B ARG* 3.6 27.0 + - - +
28B ARG* 1.3 74.9 - - - +
30B ILE* 1.3 63.5 + - + +
31B GLY* 3.2 1.7 + - - -
191B HIS* 6.0 1.9 - - - +
381B ASP* 6.2 0.2 - - - -
385B LYS* 4.4 21.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 30 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ARG* 3.0 23.9 + - + +
27B VAL* 3.5 16.4 - - - +
28B ARG 3.2 0.4 - - - -
29B GLU* 1.3 76.7 - - + +
31B GLY* 1.3 56.2 + - - +
32B VAL* 4.7 0.7 - - + -
191B HIS* 4.2 8.1 - - + +
194B LEU* 4.0 15.5 - - + +
195B ALA* 3.7 38.4 - - + +
198B VAL* 4.7 11.9 - - + -
199B ILE* 3.9 30.9 - - + +
206B PRO* 3.4 15.4 - - - +
----------------------------------------------------------
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