Contacts of the helix formed by residues 16 - 27 (chain B) in PDB entry 1GXD
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 THR 16 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B PRO 3.9 3.7 + - - -
15B LYS* 1.3 71.7 - - - +
17B ASP* 1.3 55.8 + - - +
18B LYS* 4.9 3.1 - - + +
19B GLU* 3.0 30.2 + - - +
20B LEU* 2.7 33.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 17 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B LYS 3.1 6.3 + - - -
16B THR* 1.3 70.5 - - - +
18B LYS* 1.3 66.9 + - + +
20B LEU* 3.0 20.5 + - - +
21B ALA* 3.1 5.0 + - - +
61B ASP* 4.7 6.1 - - - +
65B ILE* 2.7 44.0 - - - +
69B ARG* 2.9 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 18 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B THR* 3.3 4.4 - - + +
17B ASP* 1.3 77.7 - - + +
19B GLU* 1.3 68.1 + - - +
21B ALA* 2.7 22.8 + - + +
22B VAL* 2.8 20.6 + - + +
38B LEU* 6.3 1.0 - - - +
45B LEU* 5.7 6.0 - - - +
59B ASP* 5.8 5.1 - - - +
61B ASP* 3.8 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 19 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B LYS* 5.0 5.6 - - + -
16B THR* 3.0 37.4 + - - +
18B LYS* 1.3 76.8 - - - +
20B LEU* 1.3 64.4 + - - +
22B VAL* 3.4 17.1 + - - +
23B GLN* 3.1 43.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 20 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B LYS* 4.9 16.4 - - + -
16B THR 2.7 15.2 + - - +
17B ASP* 3.1 10.8 - - - +
18B LYS 2.9 0.2 + - - -
19B GLU* 1.3 73.0 - - - +
21B ALA* 1.3 59.6 + - - +
23B GLN* 3.3 10.4 + - + +
24B TYR* 2.9 32.1 + - + +
65B ILE* 4.0 17.9 - - + -
68B MET* 4.3 21.1 - - + +
69B ARG* 3.0 52.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 21 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B ASP 3.1 7.9 + - - +
18B LYS* 2.7 20.7 + - + +
20B LEU* 1.3 71.5 - - - +
22B VAL* 1.3 53.6 + - + +
24B TYR 2.8 4.7 + - - -
25B LEU* 2.6 48.3 + - + +
45B LEU* 4.8 5.6 - - + -
61B ASP* 5.0 6.3 - - - +
65B ILE* 5.4 0.4 - - + -
68B MET* 3.6 33.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 22 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B LYS* 2.8 25.1 + - + +
19B GLU* 3.5 21.3 - - - +
21B ALA* 1.3 73.6 - - + +
23B GLN* 1.3 61.6 + - - +
25B LEU* 3.9 7.3 - - + +
26B ASN* 3.2 21.5 + - + +
31B CYS 4.4 4.5 - - - +
32B PRO 5.0 2.7 - - - +
35B SER* 3.6 43.7 - - - +
36B CYS* 5.1 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 23 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B LYS* 6.1 0.9 - - - -
19B GLU* 3.1 31.8 + - - +
20B LEU* 3.6 13.1 - - + +
21B ALA 3.0 0.8 - - - -
22B VAL* 1.3 75.0 - - - +
24B TYR* 1.3 60.7 + - - +
25B LEU 2.9 10.0 + - - -
26B ASN* 3.0 15.5 + - + +
27B THR* 3.3 23.6 + - - +
156B ASP* 5.1 10.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 24 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B LEU* 2.9 22.8 + - + +
21B ALA 2.8 5.1 + - - +
23B GLN* 1.3 75.6 - - - +
25B LEU* 1.3 58.6 + - + +
28B PHE* 3.3 29.1 - + - -
29B TYR* 3.8 10.1 - + - -
48B MET* 3.7 25.4 - - + -
52B PHE* 3.4 13.0 - + - -
67B THR 4.5 6.6 + - - -
68B MET* 3.4 53.4 - - + -
70B LYS 5.1 2.5 - - - -
72B ARG* 2.6 52.8 + - + -
395B ILE* 4.6 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 25 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ALA* 2.6 27.9 + - + +
22B VAL* 4.3 1.8 - - + +
24B TYR* 1.3 82.3 - - + +
26B ASN* 1.3 53.2 - - - +
29B TYR* 1.9 48.2 + - + +
31B CYS* 4.2 0.4 - - - -
36B CYS* 3.8 27.6 - - - -
38B LEU* 3.9 20.0 - - + -
44B THR* 3.3 31.9 - - + -
45B LEU* 3.9 19.3 - - + +
48B MET* 3.9 25.4 - - + -
68B MET* 5.3 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 26 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B VAL 3.2 17.8 + - - +
23B GLN* 3.0 8.1 + - + +
25B LEU* 1.3 75.3 - - - +
27B THR* 1.3 78.7 + - - +
29B TYR 2.8 23.6 - - - +
30B GLY* 3.4 6.1 + - - -
31B CYS* 3.2 14.0 + - - +
32B PRO* 3.2 36.8 - - - +
81B TYR* 4.2 8.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 27 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B GLN* 3.3 18.1 + - - +
26B ASN* 1.3 88.3 + - - +
28B PHE* 1.3 91.2 + - + +
74B GLY 4.1 12.8 - - - +
76B PRO* 3.9 9.2 - - + +
81B TYR* 3.7 19.2 - - - -
161B LEU* 5.1 10.6 - - + +
----------------------------------------------------------
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