Contacts of the strand formed by residues 26 - 36 (chain C) in PDB entry 2X7N
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 26 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C CYS* 2.9 27.3 - - - +
22C ASP* 4.5 3.6 - - - +
24C SER* 3.2 13.7 + - - +
25C GLY* 1.3 79.5 + - - +
27C ARG* 1.4 59.3 + - - +
29C LEU* 4.0 17.9 - - + -
57C VAL* 3.8 24.9 - - + -
59C LYS 3.8 4.0 - - - -
60C GLY* 4.2 1.1 - - - -
64C LEU* 3.9 5.3 - - + +
97C ILE* 4.0 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 27 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C ASN* 3.2 13.5 - - - +
20C CYS* 3.0 23.7 + - - +
25C GLY 3.8 1.3 + - - +
26C ALA* 1.4 72.8 - - - +
28C ASN* 1.3 61.1 + - + +
59C LYS* 2.8 53.0 + - + +
60C GLY* 3.8 12.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 28 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C ILE* 4.0 16.9 - - + +
18C MET 3.3 11.2 - - - +
19C ASN* 5.0 1.3 - - - -
20C CYS 4.5 0.2 - - - +
27C ARG* 1.3 82.5 - - + +
29C LEU* 1.3 69.3 + - - +
57C VAL 3.9 0.2 - - - -
58C LYS* 2.7 37.9 + - - +
59C LYS* 2.6 54.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 29 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C ALA 3.7 0.3 - - - +
17C ILE* 3.2 6.5 - - - +
18C MET* 2.7 54.9 + - + +
20C CYS* 4.0 28.7 - - + -
26C ALA* 4.0 13.9 - - + -
28C ASN* 1.3 85.5 - - - +
30C TYR* 1.4 60.6 + - - +
31C ILE* 5.6 0.4 - - + -
55C ALA* 4.1 19.5 - - + -
56C THR 3.6 6.5 - - - +
57C VAL* 3.8 27.4 - - + -
58C LYS* 5.0 1.6 - - - -
71C ALA* 4.4 13.2 - - + -
95C GLY 4.7 6.5 - - - +
97C ILE* 4.2 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 30 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C VAL* 5.1 2.9 - - + -
15C GLY* 2.8 46.2 + - - -
16C ALA 3.3 3.4 - - - -
17C ILE* 4.0 18.2 - - + -
29C LEU* 1.4 74.7 - - - +
31C ILE* 1.4 72.9 + - - +
32C ILE* 3.3 5.4 + - + -
55C ALA* 3.2 4.6 - - - -
56C THR* 3.0 49.5 + - + +
58C LYS* 4.9 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 31 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C LEU* 3.9 18.6 - - + -
13C PRO 2.7 37.7 - - - +
14C VAL* 2.9 9.9 - - + +
15C GLY* 2.6 31.7 + - - +
16C ALA* 2.9 17.9 + - + +
18C MET* 3.2 34.1 - - + -
29C LEU 5.4 0.2 - - - -
30C TYR* 1.4 77.3 - - - +
32C ILE* 1.3 59.8 + - - +
33C ALA 4.8 0.2 - - - +
34C VAL* 4.9 3.4 - - + -
45C PRO 5.4 0.2 - - - +
47C ALA* 4.1 20.6 - - + +
53C VAL* 3.6 26.5 - - + -
54C MET 3.9 2.0 - - - +
55C ALA* 4.8 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 32 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C VAL* 2.9 25.7 - - + +
30C TYR* 3.3 8.8 + - + +
31C ILE* 1.3 71.7 - - - +
33C ALA* 1.4 73.1 + - + +
54C MET* 2.8 69.1 + - + +
55C ALA* 3.8 5.4 - - - +
56C THR* 5.1 7.2 - - - +
68C VAL* 5.2 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 33 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C VAL* 4.2 8.9 - - - +
31C ILE* 3.7 1.2 - - - -
32C ILE* 1.4 92.4 - - + +
34C VAL* 1.4 69.3 + - - +
35C LYS* 4.0 13.0 - - + -
45C PRO* 5.7 1.6 - - + -
53C VAL* 2.7 23.3 - - - +
54C MET* 2.8 14.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 34 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C VAL* 5.1 1.7 - - + +
31C ILE* 4.9 4.0 - - + -
33C ALA* 1.4 78.7 - - - +
35C LYS* 1.3 65.2 + - - +
37C SER* 3.8 12.8 - - - +
38C GLY* 3.3 28.4 - - - +
39C SER* 3.4 22.4 + - - +
45C PRO* 4.6 7.4 - - + +
46C ALA 3.8 15.7 - - - +
47C ALA* 2.9 37.9 - - + -
51C ASP* 4.9 0.9 - - + -
52C MET 3.8 5.2 - - - +
53C VAL* 4.4 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 35 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C ALA* 4.0 12.0 + - + -
34C VAL* 1.3 76.7 - - - +
36C GLY* 1.3 62.6 + - - +
37C SER 3.0 7.3 + - - -
38C GLY* 3.2 9.7 + - - -
52C MET* 3.0 14.0 + - + +
53C VAL* 5.2 0.9 - - - -
54C MET* 3.6 45.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 36 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C ALA* 5.6 7.7 - - - +
35C LYS* 1.3 75.6 - - - +
37C SER* 1.3 64.0 + - - -
50C GLY 4.6 1.9 - - - +
51C ASP* 3.9 3.3 - - - +
52C MET* 3.1 41.1 + - - +
121C TRP* 5.9 2.1 - - - -
----------------------------------------------------------
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