Contacts of the strand formed by residues 11 - 22 (chain C) in PDB entry 4IYC
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 ALA 11 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C ASN* 3.4 8.2 + - - -
7C ILE* 3.0 24.8 + - + +
8C GLY 2.9 16.9 + - - +
9C ASP 3.3 0.4 - - - -
10C GLY* 1.4 78.6 - - - +
12C GLU* 1.4 63.1 + - - +
36C VAL* 6.0 0.2 - - + -
37C LYS 3.3 8.7 - - - +
38C ASP* 3.8 24.9 - - + +
113C ILE* 3.9 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 12 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C ILE* 3.2 32.1 - - + +
5C GLU 3.1 15.5 - - - +
6C ASN* 3.9 17.6 - - + +
7C ILE* 4.0 3.3 - - - +
11C ALA* 1.4 76.7 - - - +
13C VAL* 1.3 65.8 + - - +
14C VAL* 4.5 6.0 - - + +
36C VAL* 4.1 1.0 - - - +
37C LYS* 3.0 45.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 13 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C ILE* 3.6 4.8 - - - -
5C GLU* 2.7 35.1 + - + +
7C ILE* 3.9 15.5 - - + -
12C GLU* 1.3 75.5 - - - +
14C VAL* 1.3 62.8 + - - +
15C LYS* 3.7 12.6 + - + +
34C ASP* 3.7 31.4 - - + -
35C PHE 3.4 7.2 - - - +
36C VAL* 4.5 12.8 - - + -
131C TYR* 3.6 50.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 14 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C ASN 4.2 3.8 - - - +
4C ILE* 4.0 23.8 - - + +
12C GLU* 4.5 9.2 - - + +
13C VAL* 1.3 71.7 - - - +
15C LYS* 1.3 58.0 + - - +
16C ARG* 3.4 28.0 - - - +
34C ASP* 3.5 0.7 - - - -
35C PHE* 2.8 57.5 + - + +
37C LYS* 4.9 5.2 - - + -
276C HIS* 3.6 41.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 15 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C ASN* 3.1 44.9 + - + +
4C ILE 5.2 0.6 + - - +
5C GLU* 2.8 40.8 + - + +
13C VAL* 4.0 10.1 - - + +
14C VAL* 1.3 73.8 - - - +
16C ARG* 1.3 68.7 + - - +
17C THR* 5.5 0.4 - - - -
34C ASP* 3.4 25.8 - - - +
131C TYR* 3.4 25.2 + - - -
133C LYS* 5.6 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 16 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C ASN* 4.2 19.8 + - - +
14C VAL* 3.4 23.6 - - + +
15C LYS* 1.3 87.6 + - - +
17C THR* 1.4 65.0 + - - +
32C GLN* 3.6 2.4 - - - +
33C PHE* 2.8 39.7 + - + +
34C ASP* 4.5 1.0 - - - +
35C PHE* 4.3 8.3 - - + -
275C THR 4.1 11.9 + - - -
276C HIS* 3.1 30.8 + - - +
277C GLU* 4.7 3.9 - - - +
278C ILE* 3.9 22.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 17 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C LYS 5.5 0.2 - - - -
16C ARG* 1.4 78.3 + - - +
18C GLU* 1.3 75.9 + - - +
19C ASP* 5.6 1.3 - - + -
30C ASN* 4.2 24.5 - - - +
31C ILE 3.3 12.3 - - - +
32C GLN* 3.9 16.4 + - + +
33C PHE* 4.6 1.8 - - - -
278C ILE* 5.7 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 18 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C THR* 1.3 81.1 - - - +
19C ASP* 1.4 70.0 + - - +
20C THR* 5.2 0.9 - - - -
29C GLN 3.4 4.0 - - - +
30C ASN* 3.6 1.1 - - - -
31C ILE* 2.8 37.7 + - - +
33C PHE* 3.8 7.2 - - + -
269C TYR* 3.8 22.9 + - + -
278C ILE* 3.6 42.2 - - + +
279C LYS* 4.6 0.2 - - - -
280C VAL* 4.0 24.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 19 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C THR* 5.0 1.5 - - + +
18C GLU* 1.4 79.3 + - - +
20C THR* 1.3 65.2 + - - +
21C SER* 4.3 12.1 + - - -
28C THR* 3.9 16.1 - - - +
29C GLN 3.4 2.6 - - - +
30C ASN* 2.8 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 20 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C GLU* 5.0 0.4 - - - +
19C ASP* 1.3 77.6 + - - +
21C SER* 1.4 60.3 + - - +
28C THR* 3.6 0.3 - - - -
29C GLN* 2.8 40.8 + - + +
265C TYR* 2.7 30.9 + - - -
267C VAL* 3.8 21.5 - - + +
269C TYR* 3.4 29.6 - - + +
280C VAL* 5.0 9.9 - - + +
283C HIS* 5.1 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 21 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C ASP* 4.3 5.8 + - - -
20C THR* 1.4 72.7 + - - +
22C SER* 1.4 62.0 + - - +
23C ASP* 4.3 6.9 - - - +
27C VAL 3.3 4.9 - - - -
28C THR* 3.0 33.1 + - - +
265C TYR* 3.7 10.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 22 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C SER* 1.4 75.9 - - - +
23C ASP* 1.3 54.1 + - - +
24C LYS* 3.7 7.4 + - - +
25C TRP* 3.2 29.0 + - - -
26C GLY* 2.7 35.9 + - - -
27C VAL 2.8 11.7 + - - -
265C TYR* 3.7 34.1 - - - -
284C ASN 5.2 1.4 - - - -
----------------------------------------------------------
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