Contacts of the helix formed by residues 18 - 31 (chain B) in PDB entry 3L6D
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 18 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B GLY 3.6 2.8 + - - -
17B LEU* 1.3 75.1 - - - +
19B ALA* 1.3 61.5 + - - -
20B MSE 3.2 2.6 + - - -
21B GLY 3.5 2.5 + - - +
22B THR* 2.8 30.2 + - - -
44B LYS* 3.8 11.9 - - - -
72B VAL 5.2 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 19 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B GLY* 1.3 71.6 - - - +
20B MSE 1.3 58.0 + - - +
22B THR* 3.8 4.9 - - - -
23B ILE* 3.0 28.8 + - - +
44B LYS* 4.5 8.0 - - - +
131B PRO* 4.9 13.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 20 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B GLY 3.3 0.2 - - - -
19B ALA* 1.3 74.7 - - - +
21B GLY* 1.3 62.5 + - - +
23B ILE* 3.2 6.9 + - - +
24B MSE 2.9 54.0 + - + +
72B VAL* 4.0 20.6 - - + -
100B TYR* 5.8 1.1 - - + -
127B ILE* 4.1 15.9 - - + -
129B ALA 3.8 16.6 - - - +
131B PRO* 3.8 34.3 - - + +
134B VAL* 3.5 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 21 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B VAL* 3.9 7.6 - - - +
16B GLY 3.7 22.9 - - - -
17B LEU* 4.6 1.3 - - - -
18B GLY* 3.5 4.2 + - - +
20B MSE 1.3 77.9 - - - +
22B THR* 1.3 62.3 + - - +
24B MSE 3.3 4.0 + - - +
25B ALA* 2.9 25.0 + - - +
72B VAL* 3.9 24.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 22 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B LEU* 3.4 9.3 + - - +
18B GLY 2.8 27.3 + - - -
19B ALA* 3.8 5.6 - - - -
21B GLY* 1.3 72.0 - - - +
23B ILE* 1.3 58.6 + - - +
25B ALA* 3.4 2.4 + - - +
26B GLN* 3.0 42.5 + - - +
44B LYS* 3.1 34.6 - - + +
47B ALA* 6.0 3.4 - - + -
48B LEU* 4.0 25.4 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
19B ALA 3.0 18.1 + - - +
20B MSE 3.4 10.1 - - - +
22B THR* 1.3 73.8 - - - +
24B MSE 1.3 69.0 + - - +
26B GLN* 3.1 29.3 + - + +
27B VAL* 2.9 38.0 + - + +
131B PRO* 3.7 28.5 - - + +
132B ARG* 5.9 1.8 - - - -
134B VAL* 3.7 28.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 24 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B VAL* 5.2 4.5 - - + -
20B MSE 2.9 41.4 + - + +
21B GLY* 3.6 4.7 - - - +
23B ILE* 1.3 76.0 - - - +
25B ALA* 1.3 63.5 + - - +
27B VAL* 3.8 0.7 - - - +
28B LEU* 2.9 35.0 + - + +
70B ILE* 4.0 13.9 - - + -
72B VAL* 3.9 25.6 - - - -
100B TYR* 3.7 36.3 - - + -
127B ILE* 4.1 17.0 - - + -
134B VAL* 4.0 11.0 - - + -
160B LEU* 3.8 31.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 25 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B VAL* 4.2 21.9 - - + +
21B GLY 2.9 16.7 + - - +
22B THR 3.7 3.8 - - - +
24B MSE 1.3 77.7 - - - +
26B GLN* 1.3 57.2 + - - +
28B LEU* 3.4 4.5 + - - +
29B LEU* 2.8 36.8 + - + +
35B VAL* 4.3 6.5 - - + +
37B ILE* 4.4 10.3 - - + -
48B LEU* 3.8 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 26 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B THR* 3.0 28.9 + - - +
23B ILE* 3.1 38.7 + - + +
25B ALA* 1.3 75.2 - - - +
27B VAL* 1.3 58.3 + - - +
29B LEU* 3.3 10.9 + - + +
30B LYS* 2.8 31.7 + - - +
47B ALA* 5.4 7.1 - - - +
48B LEU* 3.6 15.2 - - + +
51B ALA* 5.5 6.5 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
23B ILE* 2.9 31.2 + - + +
24B MSE 3.8 3.4 - - - +
26B GLN* 1.3 74.8 - - - +
28B LEU* 1.3 60.5 + - - +
30B LYS* 3.1 8.6 + - - +
31B GLN* 2.9 61.3 + - - +
134B VAL* 3.5 26.0 - - + +
135B GLY* 3.8 9.6 - - - +
159B GLY 3.4 12.6 - - - +
160B LEU* 4.5 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 28 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B VAL* 4.1 15.9 - - + -
14B VAL* 4.5 7.9 - - + -
24B MSE 2.9 26.2 + - - +
25B ALA* 3.8 2.9 - - - +
27B VAL* 1.3 76.3 - - - +
29B LEU* 1.4 60.8 + - - +
31B GLN* 3.2 24.2 + - - +
33B LYS* 3.1 45.5 + - + +
35B VAL* 4.0 10.3 - - + -
70B ILE* 3.9 26.9 - - + -
156B LEU* 4.0 22.0 - - + +
159B GLY* 4.6 0.7 - - - -
160B LEU* 3.9 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 29 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ALA* 2.8 28.5 + - + +
26B GLN* 3.6 7.2 - - - +
28B LEU* 1.4 72.3 - - - +
30B LYS* 1.3 64.1 + - - +
32B GLY* 3.0 15.6 + - - -
33B LYS 4.0 11.5 + - - +
34B ARG* 5.4 0.2 - - - -
35B VAL* 3.8 26.9 - - + +
48B LEU* 4.0 8.3 - - + +
51B ALA* 3.6 36.6 - - + +
52B GLY* 3.6 10.5 - - - +
53B ALA* 3.6 31.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 30 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B GLN 2.8 21.2 + - - +
27B VAL* 3.1 8.7 + - - +
29B LEU* 1.3 72.9 - - - +
31B GLN* 1.3 61.6 + - + +
32B GLY 3.2 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 31 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B VAL* 2.9 28.8 + - - +
28B LEU* 3.6 10.4 - - - +
29B LEU 3.2 0.4 - - - -
30B LYS* 1.3 77.6 - - + +
32B GLY* 1.3 58.8 + - - +
33B LYS* 2.7 43.1 + - - +
135B GLY* 4.3 7.5 + - - -
159B GLY* 2.6 39.9 + - - +
----------------------------------------------------------
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