Contacts of the strand formed by residues 17 - 24 (chain C) in PDB entry 1XE0
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 ASN 17 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C GLN* 1.3 80.2 - - - +
18C PHE* 1.3 70.0 + - - +
19C LEU 4.4 0.2 + - - -
116C GLN* 3.0 38.5 + - - +
117C HIS 3.7 2.5 - - - -
118C LEU* 3.8 6.9 - - + +
43D GLN* 3.5 24.2 - - - +
95D GLU* 3.1 26.9 + - - +
96D ILE* 4.1 2.6 - - - +
97D THR* 3.6 29.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 18 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C GLN* 3.7 33.4 - - + -
17C ASN* 1.3 82.4 + - - +
19C LEU* 1.3 64.2 + - - +
116C GLN* 3.2 5.4 - - - -
117C HIS* 2.7 47.7 + - + +
119C VAL* 3.7 13.9 - - + -
67D ILE* 4.1 7.4 - - + +
68D ASN 3.8 11.0 - - - -
69D TYR* 3.6 62.6 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 19 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C ASN 4.4 0.4 + - - -
18C PHE* 1.3 77.2 - - - +
20C PHE* 1.3 59.4 + - - +
115C GLY 3.9 2.2 - - - -
116C GLN* 5.8 0.4 - - + -
117C HIS* 4.8 1.9 - - - +
64D ALA* 4.2 13.2 - - + +
65D GLU 4.2 4.3 - - - -
66D GLY* 3.7 33.9 - - - +
67D ILE 4.0 11.6 + - - +
68D ASN* 3.8 13.3 - - - +
69D TYR 4.7 0.3 + - - -
74D ILE* 3.6 19.3 - - + +
76D ILE* 3.6 29.8 - - + -
94D PHE* 4.2 7.9 - - + -
95D GLU 5.6 0.2 - - - +
96D ILE* 3.9 39.5 - - + -
100D VAL* 4.4 6.1 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
19C LEU* 1.3 75.9 - - - +
21C GLY* 1.3 74.8 + - - +
22C CYS* 4.0 20.4 - - - -
31C TYR* 3.5 41.1 - + - -
33C PHE* 4.4 6.1 - + - -
44C LEU* 3.7 39.9 - - + -
46C LEU* 4.2 10.3 - - + -
102C LEU* 4.4 4.5 - - + -
113C VAL* 4.4 5.8 - - + -
114C SER* 3.5 0.6 - - - -
115C GLY* 3.0 52.2 + - - +
116C GLN 3.9 11.9 - - - -
117C HIS* 4.0 6.7 - + + +
74D ILE* 4.1 2.7 - - - -
76D ILE* 3.5 15.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 21 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C PHE* 1.3 90.5 - - - +
22C CYS* 1.3 64.7 + - - +
31C TYR* 4.9 4.0 + - - -
113C VAL 3.1 12.6 - - - -
74D ILE* 3.9 7.4 - - - +
75D LYS 5.8 1.6 - - - -
76D ILE* 3.7 20.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 22 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C PHE* 4.0 5.6 - - + -
21C GLY* 1.3 75.1 - - - +
23C GLU* 1.3 60.5 + - - +
24C LEU* 4.2 8.0 + - - -
28C LYS* 4.9 0.4 - - - +
31C TYR* 3.7 44.4 - - + -
102C LEU* 4.0 14.1 - - - -
111C VAL 4.0 0.2 - - - +
112C TYR* 3.4 7.6 - - - +
113C VAL* 3.0 56.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 23 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C CYS* 1.3 75.5 - - - +
24C LEU* 1.3 62.6 + - - +
25C LYS* 3.2 40.9 + - + +
28C LYS* 3.4 24.7 + - - +
110C PRO* 4.3 9.9 - - + +
111C VAL 3.5 4.9 - - - +
112C TYR* 2.7 45.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 24 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C CYS* 4.2 8.1 - - - -
23C GLU* 1.3 77.5 - - - +
25C LYS* 1.3 63.4 + - - +
28C LYS 3.5 3.1 - - - -
29C LYS 3.7 13.7 - - - +
30C GLU 3.8 4.0 - - - -
31C TYR* 3.7 33.4 - - + +
62C VAL* 4.0 23.8 - - + -
102C LEU* 3.7 5.2 - - + +
103C ARG 3.9 11.2 - - - +
104C LEU* 3.8 37.1 - - + +
110C PRO* 3.3 1.2 - - - +
111C VAL* 2.8 40.0 + - + +
113C VAL* 4.3 13.2 - - + -
----------------------------------------------------------
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