Contacts of the strand formed by residues 16 - 23 (chain A) in PDB entry 4HXG
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 16 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A PHE* 2.7 39.7 + + - +
14A PHE* 3.3 41.4 - + + -
15A ALA* 1.3 73.8 - - - +
17A LEU* 1.3 65.0 + - - +
18A SER* 5.1 0.7 - - - -
30A VAL 3.4 2.6 - - - +
31A LEU* 4.4 0.2 - - - +
32A THR* 2.8 56.5 + - + +
33A LYS* 5.0 2.5 - - - -
34A ALA* 5.2 11.2 - - + -
41A TYR* 6.2 3.1 - + - -
322A PRO* 5.0 11.9 - - + -
323A ALA 6.3 0.2 - - - +
396A PHE* 5.9 3.3 - + - -
398A TYR* 5.7 0.2 - - - -
589A ARG* 4.6 11.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 17 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ALA* 3.9 5.1 + - + +
16A TYR* 1.3 80.3 - - - +
18A SER* 1.3 64.3 + - - +
29A TYR* 4.3 15.3 - - + -
30A VAL 3.2 4.7 - - - +
31A LEU* 3.8 28.7 - - + -
315A LEU* 3.7 25.6 - - + +
323A ALA* 3.9 32.6 + - - +
324A GLU* 4.1 1.1 - - - +
325A LEU* 4.1 10.1 - - + +
336A THR* 3.6 24.0 - - - +
338A TYR* 3.9 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 18 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A TYR 5.1 1.6 - - - -
17A LEU* 1.3 77.3 - - - +
19A ASP* 1.3 69.7 + - - +
20A PRO* 3.6 3.8 - - - -
29A TYR* 3.8 1.9 - - - +
30A VAL* 2.8 49.7 + - - +
32A THR* 4.7 4.0 + - - -
315A LEU* 3.8 8.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 19 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A SER* 1.3 82.7 - - - +
20A PRO* 1.3 74.4 - - - +
21A ARG* 3.2 31.6 + - - +
28A ALA 3.8 4.9 - - - +
29A TYR* 3.8 3.7 - - - -
30A VAL* 4.2 7.9 - - + -
63A MET* 3.7 7.8 + - - +
64A PRO* 3.4 13.0 - - - +
65A ARG* 3.1 27.9 + - - -
315A LEU* 4.3 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 20 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A SER 3.6 0.4 - - - -
19A ASP* 1.3 91.7 - - - +
21A ARG* 1.3 70.6 + - - +
28A ALA 3.6 6.1 - - - +
29A TYR* 4.2 5.8 - - + -
268A LYS* 4.5 2.8 + - - -
305A GLY* 3.8 11.9 - - - +
306A PHE* 3.7 29.2 - - - +
307A ASP* 3.8 9.8 - - - +
313A ILE* 3.5 23.3 - - + -
315A LEU* 3.7 27.6 - - + +
325A LEU* 4.4 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ASP* 3.2 27.2 + - - +
20A PRO* 1.3 79.8 + - - +
22A THR* 1.3 61.6 + - - +
27A VAL* 3.3 6.2 - - - +
28A ALA* 2.9 36.6 + - + +
64A PRO* 3.5 21.5 - - + +
65A ARG* 3.2 49.6 - - - +
66A ILE* 4.2 18.3 - - + +
268A LYS* 4.9 12.3 - - - +
307A ASP* 3.4 13.2 - - - -
313A ILE* 3.9 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ARG* 1.3 76.7 - - - +
23A ARG* 1.3 79.5 + - - +
26A LEU 2.8 19.8 + - - -
27A VAL* 3.5 14.6 - - - +
66A ILE* 4.3 3.6 - - - -
307A ASP* 2.9 41.2 + - + +
308A ALA* 3.6 1.1 - - - +
309A ASP* 3.4 30.8 - - + +
311A ARG* 3.8 18.2 - - - +
313A ILE* 4.3 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A THR* 1.3 90.0 + - - +
24A LYS* 1.3 78.0 + - + +
26A LEU* 2.8 24.6 + - + +
66A ILE* 3.7 44.4 + - + +
67A SER 4.0 3.6 - - - +
68A PRO* 3.9 32.6 - - - +
70A GLY* 4.8 1.8 - - - -
307A ASP* 5.5 0.9 - - - -
309A ASP* 3.4 23.3 + - - +
----------------------------------------------------------
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