Contacts of the helix formed by residues 14 - 24 (chain C) in PDB entry 1RLI
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 14 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C THR* 3.8 23.5 + - - +
11C ARG 3.9 2.8 + - - -
12C SER 3.2 6.5 + - - -
13C GLY* 1.3 80.9 - - - +
15C ASN* 1.3 67.0 + - - -
16C THR 3.1 2.9 - - - -
17C ASP* 3.0 3.7 + - - +
18C VAL* 3.0 22.6 + - - +
158C PRO* 5.0 7.2 - - - -
609C PT 4.1 7.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 15 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C GLY 3.6 0.8 + - - -
14C GLY* 1.3 71.6 - - - +
16C THR* 1.3 61.5 + - - +
18C VAL* 3.6 1.8 + - - +
19C LEU* 3.2 28.1 + - - +
120C VAL* 3.8 22.6 - - + +
155C GLY* 3.9 15.3 - - - -
156C ASN* 4.0 2.0 - - - +
157C ARG 3.1 32.4 + - - +
158C PRO* 4.2 1.2 - - - +
159C GLY 3.3 7.7 + - - -
160C ASP* 3.3 9.0 + - - +
161C ILE* 2.9 41.7 + - + +
609C PT 3.7 7.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 16 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C ASN* 3.9 14.6 - - - +
9C GLY* 4.7 3.8 - - - -
10C THR 5.2 1.8 - - - -
14C GLY 3.1 0.4 - - - -
15C ASN* 1.3 78.7 - - - +
17C ASP* 1.3 68.2 + - - +
19C LEU* 3.5 2.5 + - - +
20C ALA* 3.1 22.9 + - - +
75C ALA* 3.6 39.2 - - + +
76C THR* 3.7 5.7 + - - +
77C PRO* 3.5 32.0 - - + +
118C ILE* 4.9 3.5 - - + +
120C VAL* 4.3 11.9 - - + +
609C PT 4.2 4.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 17 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C ASN* 3.2 25.3 + - - +
10C THR 2.6 24.1 + - - +
11C ARG* 2.9 36.6 - - - +
12C SER* 3.0 12.3 + - - +
13C GLY 4.6 2.9 - - - +
14C GLY 3.0 10.4 + - - +
16C THR* 1.3 76.5 - - - +
18C VAL* 1.3 57.6 + - + +
20C ALA* 3.5 2.0 + - - +
21C GLU* 2.9 34.4 + - - +
33C TYR* 4.0 5.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 18 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C GLY* 4.3 16.8 - - - +
14C GLY 3.0 22.4 + - - +
15C ASN* 3.8 4.7 - - - +
16C THR 3.3 0.2 - - - -
17C ASP* 1.3 74.1 - - + +
19C LEU* 1.3 66.6 + - - +
21C GLU* 3.2 8.5 + - + +
22C LYS* 3.1 41.3 + - - +
159C GLY* 6.1 2.2 - - - +
161C ILE* 3.8 22.0 - - + -
162C LEU* 4.4 15.3 - - + -
168C LEU* 4.6 1.1 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
15C ASN 3.2 10.4 + - - +
16C THR 4.1 0.4 - - - +
18C VAL* 1.3 79.3 - - - +
20C ALA* 1.3 63.4 + - - +
22C LYS* 3.3 5.8 + - + +
23C ALA* 3.1 18.7 + - - +
118C ILE* 3.7 24.6 - - + +
120C VAL* 3.6 26.9 - - + -
151C VAL* 4.3 16.2 - - + -
153C GLY* 4.4 2.9 - - - +
161C ILE* 3.6 23.6 - - + -
167C ALA* 3.8 12.6 - - + +
168C LEU* 3.8 28.5 - - + -
171C ALA* 3.7 26.3 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
5C VAL* 3.9 26.5 - - + -
7C ASN* 5.0 3.4 - - - +
16C THR 3.1 17.0 + - - +
17C ASP* 3.8 4.5 - - - +
19C LEU* 1.3 78.1 - - - +
21C GLU* 1.3 64.0 + - - +
23C ALA* 3.0 12.9 + - - +
24C VAL* 3.1 19.7 + - - +
73C ILE* 5.4 0.2 - - + -
75C ALA* 4.1 14.6 - - + -
118C ILE* 3.6 14.2 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
17C ASP* 2.9 21.1 + - - +
18C VAL* 3.2 10.1 + - - +
20C ALA* 1.3 77.4 - - - +
22C LYS* 1.3 58.5 + - + +
24C VAL* 3.4 7.7 + - - +
25C GLN* 2.8 36.8 + - + +
31C HIS* 4.3 18.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 22 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C VAL* 3.1 21.4 + - + +
19C LEU* 3.6 6.7 - - - +
20C ALA 3.2 0.2 - - - -
21C GLU* 1.3 78.9 - - + +
23C ALA* 1.3 63.6 + - - +
25C GLN* 3.3 31.4 + - - +
162C LEU* 4.8 6.6 - - - +
168C LEU* 2.9 64.7 - - + +
171C ALA* 4.3 12.2 - - + +
172C SER* 4.6 15.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 23 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C LEU 3.1 12.0 + - - +
20C ALA 3.0 10.0 + - - +
22C LYS* 1.3 79.0 - - - +
24C VAL* 1.3 64.6 + - + +
25C GLN 3.8 0.2 + - - -
27C PHE* 4.1 6.9 - - - -
73C ILE* 4.4 5.8 - - + -
118C ILE* 3.8 18.8 - - + -
171C ALA 3.4 21.6 + - - +
172C SER* 5.1 2.5 - - - +
174C LEU* 4.4 11.7 - - + -
175C LEU* 3.4 21.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 24 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C ILE* 4.2 11.0 - - + -
5C VAL* 3.4 24.9 - - + -
20C ALA 3.1 15.0 + - - +
21C GLU* 3.8 7.4 - - - +
23C ALA* 1.3 76.2 - - - +
25C GLN* 1.3 67.6 + - - +
26C GLY 3.2 0.5 + - - -
27C PHE* 3.0 30.3 + - + +
29C ALA* 4.1 9.4 - - + -
31C HIS* 4.2 22.4 - - + +
73C ILE* 3.4 32.3 - - + -
175C LEU* 4.3 2.7 - - + -
----------------------------------------------------------
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