Contacts of the strand formed by residues 14 - 20 (chain C) in PDB entry 6P7B
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 14 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C VAL* 3.3 7.9 - - - +
7C ASP* 2.9 33.7 + - + +
12C ASN 3.7 0.6 + - - -
13C PRO* 1.3 76.3 - - - +
15C TYR* 1.3 64.2 + - - +
33C GLU 3.4 12.6 - - - +
34C LYS* 4.3 2.0 - - - -
35C SER 4.5 0.7 - - - +
37C TRP* 6.3 0.4 - - - -
132C ASP* 3.9 38.6 - - + +
133C ILE* 3.9 12.6 - - + +
136C SER* 4.3 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 15 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C CYS* 4.6 6.1 - - - -
5C SER 3.2 10.1 - - - +
6C VAL* 4.3 13.0 - - + -
13C PRO 5.9 0.2 - - - -
14C ALA* 1.3 77.1 - - - +
16C ALA* 1.3 59.9 + - - +
17C ILE* 3.6 31.2 - - + -
31C ALA* 5.2 1.6 - - + -
32C ILE* 3.5 3.6 - - - +
33C GLU* 2.9 75.5 + - + +
35C SER* 4.1 22.9 - - - -
37C TRP* 5.9 3.6 - + + -
48C ASP* 4.2 28.3 + - + -
49C LEU* 5.9 1.1 - - + -
51C ARG* 3.6 26.9 + - - -
52C TYR* 4.2 10.2 - + - -
133C ILE* 5.5 0.2 - - - +
136C SER* 4.2 4.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 16 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C ILE 3.6 1.2 - - - +
4C CYS* 3.4 3.8 - - - -
5C SER* 2.9 46.5 + - - +
15C TYR* 1.3 74.0 - - - +
17C ILE* 1.3 61.4 + - - +
18C PHE* 3.7 21.7 - - + -
29C LEU* 4.6 0.7 - - + -
31C ALA 3.6 5.2 - - - +
32C ILE* 3.6 20.9 - - + -
136C SER* 4.2 8.9 + - - +
137C PHE* 4.4 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 17 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C ILE* 3.9 19.1 - - + -
3C ILE 3.4 2.5 - - - +
4C CYS* 3.5 34.8 - - + -
15C TYR* 3.6 24.7 - - + -
16C ALA* 1.3 72.8 - - - +
18C PHE* 1.3 57.6 + - - +
29C LEU* 3.2 3.3 - - - +
30C ILE* 2.7 40.0 + - + -
31C ALA* 2.9 21.6 + - + +
48C ASP 5.4 2.7 - - - +
52C TYR* 3.5 51.4 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
2C ILE* 3.5 9.7 - - - +
3C ILE* 2.9 52.6 + - + +
5C SER* 3.8 11.0 - - - -
16C ALA* 3.7 25.1 - - + -
17C ILE* 1.3 75.2 - - - +
19C ASN* 1.3 61.8 + - - +
20C TYR 4.2 0.2 - - - -
27C ILE* 4.0 27.4 - - + -
28C LYS 3.4 6.3 - - - +
29C LEU* 3.6 22.7 - - + -
30C ILE* 4.1 3.6 - - - +
116C TYR* 5.0 2.5 - + - -
137C PHE* 3.4 49.6 - + - -
140C GLY* 4.1 12.1 - - - -
141C LEU* 4.6 8.1 - - + -
144C MET* 4.8 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 19 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C MET 3.7 12.7 + - - +
2C ILE* 4.3 10.0 - - - +
18C PHE* 1.3 76.5 - - - +
20C TYR* 1.3 68.4 + - - +
21C ASP* 3.9 4.3 + - - +
26C THR 3.4 3.3 - - - +
27C ILE* 3.7 0.8 - - - -
28C LYS* 2.5 76.4 + - + +
30C ILE* 3.6 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 20 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C MET* 2.7 54.6 + - + +
3C ILE* 4.7 4.5 - - + -
18C PHE 4.2 0.4 - - - -
19C ASN* 1.3 75.9 + - - +
21C ASP* 1.3 71.3 + - - +
22C ASN* 3.3 22.4 + - - -
23C THR* 4.6 4.6 + - - -
25C ASN* 2.3 52.2 + - + -
26C THR 3.5 7.9 - - - -
27C ILE* 4.4 3.8 - - + -
144C MET* 3.4 32.8 - - + -
147C LEU* 3.7 30.4 - - + +
148C LEU* 4.9 6.6 - - - +
----------------------------------------------------------
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