Contacts of the strand formed by residues 17 - 24 (chain C) in PDB entry 5IXG
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 17 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C PRO 3.7 8.5 + - - -
14C SER* 2.9 36.4 + - - -
15C HIS* 3.9 4.5 - - - -
16C THR* 1.4 83.4 - - - +
18C PRO* 1.3 67.0 - - + +
19C SER* 3.7 3.3 + - - +
34C LYS* 3.4 32.8 - - - +
35C PHE 3.5 16.6 - - - +
36C ASP* 3.4 22.2 - - - -
166C LEU 3.9 0.5 - - - +
167C ILE* 3.8 0.2 - - - -
168C THR* 2.9 43.0 + - + +
201C OTP 4.5 3.6 - - - -
31D TRP* 3.8 17.1 - + - -
64D THR 4.2 0.7 - - - -
65D GLY* 3.6 31.3 + - - -
66D SER* 3.8 9.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 18 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C TYR* 1.3 81.9 - - - +
19C SER* 1.3 63.6 + - - +
34C LYS* 3.4 2.6 - - - +
35C PHE* 3.1 49.1 + - + +
38C SER* 3.6 17.5 - - - +
57C THR* 3.8 18.4 - - + +
165C LEU* 5.1 1.3 - - + -
167C ILE* 3.7 26.2 - - + -
201C OTP 3.9 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 19 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C TYR* 3.7 2.5 + - - +
18C PRO* 1.3 75.4 - - - +
20C PHE* 1.3 64.2 + - - +
33C GLY 3.2 12.6 - - - -
34C LYS* 3.6 17.9 - - - +
165C LEU* 3.4 8.4 - - - +
166C LEU* 2.8 42.1 + - - -
168C THR* 5.2 1.7 + - - -
32D ARG* 3.8 34.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 20 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C PRO 5.3 0.2 - - - -
19C SER* 1.3 79.3 - - - +
21C GLU* 1.4 70.3 + - - +
31C TRP* 4.3 7.2 - + + -
32C ARG* 3.3 22.6 - - - +
33C GLY* 2.8 41.9 + - - +
34C LYS* 3.4 9.9 - - - -
35C PHE* 3.8 32.5 - + - -
62C ILE* 3.9 21.8 - - + -
64C THR* 4.3 7.6 - - + -
163C THR* 4.5 3.8 - - + -
164C LYS 3.1 12.1 - - - +
165C LEU* 4.3 9.9 - - + -
166C LEU* 4.4 2.9 - - - +
201C OTP 3.8 45.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 21 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C PHE* 1.4 77.8 - - - +
22C ALA* 1.3 61.8 - - - +
30C VAL* 3.8 11.8 - - + +
31C TRP 3.2 5.4 - - - -
32C ARG* 3.2 41.1 + - + +
162C LYS 4.2 1.2 - - - +
163C THR* 3.5 6.6 - - - +
164C LYS* 2.9 62.9 + - + +
166C LEU* 3.9 19.9 - - + +
166D LEU* 4.2 8.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 22 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C PHE* 4.8 0.9 - - + -
21C GLU* 1.3 76.9 - - - +
23C ASP* 1.4 62.9 + - - +
30C VAL* 3.5 6.4 - - - +
31C TRP* 2.7 42.9 + - + +
146C ARG* 5.5 2.5 - - - +
162C LYS 4.6 5.4 - - - -
163C THR* 4.8 7.9 - - + +
201C OTP 3.6 44.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 23 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C ALA* 1.4 75.2 - - - +
24C HIS* 1.3 61.1 + - - +
25C PHE 3.5 0.3 + - - -
26C GLY* 2.9 25.0 + - - -
27C GLY* 2.7 28.0 + - - -
29C SER 3.9 5.6 - - - +
30C VAL* 4.9 2.8 - - - +
31C TRP* 4.4 1.8 - - - -
146C ARG* 5.0 0.3 + - - -
159C PHE* 3.4 19.2 - - - -
160C LYS* 2.9 54.5 + - + +
162C LYS 4.6 4.8 + - - +
201C OTP 4.1 11.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 24 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C ALA 3.7 0.2 + - - -
23C ASP* 1.3 73.0 - - - +
25C PHE* 1.3 99.8 + + - +
26C GLY 3.4 1.9 + - - -
28C LEU* 3.1 23.8 + - + +
29C SER* 3.0 23.9 + - - +
31C TRP* 4.0 13.5 - - + -
159C PHE* 3.7 15.0 - + - -
201C OTP 3.4 25.9 + - - -
15D HIS* 3.2 29.9 + + - -
170D GLU* 2.6 34.4 + - - -
----------------------------------------------------------
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