Contacts of the helix formed by residues 13 - 25 (chain C) in PDB entry 2RCY
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 13 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C GLY 3.6 4.2 + - - -
12C LEU* 1.3 78.0 - - - +
14C GLN* 1.3 58.0 + - - -
15C MSE 3.5 1.8 - - - -
16C GLY* 4.2 4.4 - - - +
17C SER* 2.7 29.6 + - - -
65C ALA 5.0 0.6 + - - -
264C NAP 3.2 37.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 14 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B GLN* 5.6 2.4 + - - +
221B ASP 5.5 0.2 - - - +
222B ASN* 3.1 64.2 + - + +
13C GLY* 1.3 74.3 - - - -
15C MSE 1.3 62.0 + - - +
17C SER* 3.5 7.2 + - - -
18C ALA* 3.4 18.9 - - - +
116C THR* 4.4 6.1 - - + +
264C NAP 3.0 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 15 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C GLN* 1.3 75.8 - - - +
16C GLY* 1.3 67.1 + - - +
17C SER 3.4 0.2 - - - -
18C ALA* 4.0 4.3 - - + -
19C LEU* 3.0 31.6 + - + +
90C ILE* 3.7 19.5 - - + -
114C PRO* 4.0 11.0 - - + -
115C ASN* 3.5 25.1 - - - +
116C THR* 3.7 17.0 - - - +
118C CYS* 3.5 20.2 - - - -
264C NAP 3.0 72.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 16 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C PHE* 4.2 4.2 - - - -
11C GLY 3.8 20.2 - - - -
12C LEU* 3.4 8.7 - - - +
13C GLY 4.0 7.1 + - - +
14C GLN 3.6 0.2 - - - -
15C MSE 1.3 79.1 - - - +
17C SER* 1.3 55.2 + - - +
19C LEU* 3.5 3.9 + - - +
20C ALA* 2.9 30.5 + - - +
65C ALA* 3.9 16.6 - - - +
90C ILE* 5.0 0.9 - - - -
264C NAP 4.1 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 17 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C LEU* 3.7 20.7 - - - +
13C GLY 2.7 25.7 + - - -
14C GLN* 3.5 7.8 + - - -
16C GLY* 1.3 72.6 - - - +
18C ALA* 1.3 63.2 + - - +
20C ALA* 4.2 0.7 - - - -
21C HIS* 2.8 58.1 + - - -
119C LEU* 5.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 18 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C GLN 3.4 17.2 + - - +
15C MSE 3.4 13.4 + - + +
16C GLY 3.4 0.4 - - - -
17C SER* 1.3 81.9 + - - +
19C LEU* 1.3 57.1 + - - +
22C GLY* 3.1 22.3 + - - -
116C THR* 3.9 26.7 - - - +
118C CYS* 3.4 10.4 - - - -
119C LEU* 3.6 24.3 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
9C PHE* 3.8 21.5 - - + -
15C MSE 3.0 21.7 + - + +
16C GLY* 3.9 3.1 - - - +
18C ALA* 1.3 73.8 - - - +
20C ALA* 1.3 65.3 + - - +
22C GLY* 3.8 0.5 - - - -
23C ILE* 3.1 38.0 + - + +
63C VAL* 4.4 6.7 - - + -
90C ILE* 4.1 29.4 - - + -
114C PRO* 4.5 5.4 - - + -
118C CYS* 3.5 12.3 - - + -
125C PHE* 3.8 21.5 - - + -
145C PHE* 3.6 35.7 - - + -
148C CYS* 4.8 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 20 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C PHE* 3.7 17.1 - - + -
12C LEU* 3.8 12.6 - - + -
16C GLY 2.9 19.3 + - - +
17C SER* 3.4 4.0 + - - +
19C LEU* 1.3 77.4 - - - +
21C HIS* 1.3 58.6 + - + +
23C ILE* 3.5 2.8 + - - +
24C ALA* 3.0 26.9 + - - +
34C LEU* 4.7 2.9 - - - +
46C LEU* 3.7 35.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 21 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C LEU* 5.1 0.9 - - + +
17C SER* 2.8 44.2 + - - +
20C ALA* 1.3 69.4 - - - +
22C GLY* 1.3 60.0 - - - +
24C ALA* 3.8 5.6 - - + -
25C ASN* 3.0 41.2 + - - +
43C ASN 4.5 7.9 - - - -
44C THR* 2.8 39.2 + - - -
45C THR* 4.0 14.3 + - + -
46C LEU* 4.0 10.9 - - + +
119C LEU* 3.8 21.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 22 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C ALA 3.1 15.5 + - - -
19C LEU 3.4 1.8 + - - -
20C ALA 3.2 0.4 - - - -
21C HIS* 1.3 77.6 - - - +
23C ILE* 1.3 59.5 + - - +
25C ASN* 3.8 3.3 + - - +
26C ALA* 3.5 15.2 + - - +
118C CYS 3.3 24.5 - - - -
119C LEU* 4.2 7.4 - - - +
121C GLY* 5.5 1.1 - - - -
148C CYS* 3.4 19.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 23 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C LEU* 4.0 9.9 - - + -
9C PHE* 3.7 22.7 - - + -
19C LEU* 3.1 29.6 + - + +
20C ALA 3.9 3.1 - - - +
22C GLY* 1.3 73.3 - - - +
24C ALA* 1.3 65.7 + - - +
26C ALA* 3.2 18.9 + - - +
27C ASN* 3.5 5.9 + - - -
28C ILE* 4.0 27.3 + - + +
29C ILE* 4.2 17.6 + - + +
34C LEU* 4.5 9.4 - - + -
63C VAL* 6.3 0.2 - - + -
144C ILE* 3.8 26.7 - - + +
145C PHE* 4.9 2.0 - - + -
147C SER* 4.6 0.4 - - - -
148C CYS* 4.1 16.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 24 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C ALA 3.0 19.0 + - - +
21C HIS* 3.7 10.5 - - - +
22C GLY 3.4 0.2 - - - -
23C ILE* 1.3 76.7 - - - +
25C ASN* 1.3 61.6 + - - +
26C ALA 3.4 0.7 + - - -
27C ASN* 3.0 24.1 + - - +
29C ILE 5.5 2.2 - - - +
34C LEU* 3.9 23.5 - - + +
45C THR* 4.5 19.5 - - + -
46C LEU* 4.8 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 25 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C HIS* 3.0 28.8 + - - +
22C GLY* 4.2 4.0 - - - +
23C ILE 3.3 0.2 - - - -
24C ALA* 1.3 78.6 - - - +
26C ALA* 1.3 62.1 + - - +
27C ASN* 3.3 8.8 - - - +
119C LEU* 4.1 16.6 + - - +
----------------------------------------------------------
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