Contacts of the strand formed by residues 29 - 38 (chain C) in PDB entry 4A4C
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 ASP 29 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C PRO* 3.7 6.8 - - - +
26C VAL 3.5 11.8 + - - +
27C GLY 3.4 2.2 - - - -
28C ASP* 1.3 74.3 - - - +
30C MET* 1.3 63.1 + - - +
31C PHE* 3.3 29.1 + - - +
32C HIS* 3.3 38.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 30 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C LEU* 4.1 20.9 - - + -
6C ILE* 3.2 40.4 - - + +
7C HIS* 3.3 42.8 - - + +
10C LEU* 4.2 18.6 - - + -
25C PRO* 3.9 19.5 - - - -
28C ASP 3.5 8.5 + - - +
29C ASP* 1.3 73.4 + - - +
31C PHE* 1.3 62.2 + - + +
32C HIS 3.4 0.4 - - - -
33C TRP* 2.9 28.2 + - + +
56C PHE* 3.9 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 31 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C ALA* 5.7 1.3 - - + -
3C LEU* 3.9 35.2 - - + -
6C ILE* 3.8 17.3 - - + -
29C ASP* 3.1 20.6 - - - +
30C MET* 1.3 82.8 - - + +
32C HIS* 1.3 58.2 + - - +
54C ILE 3.3 4.5 - - - +
55C HIS* 3.3 12.9 + + + +
56C PHE* 3.0 60.1 + - + +
57C PRO 4.7 6.5 - - - -
58C THR* 5.0 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 32 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C PRO* 3.3 1.2 - - - +
26C VAL* 2.9 52.7 + - + +
29C ASP* 3.3 23.6 + - + +
31C PHE* 1.3 79.8 - - - +
33C TRP* 1.3 86.9 + - - +
34C GLN* 5.1 1.8 - - + +
53C THR* 3.1 34.4 - - + +
54C ILE 3.4 7.4 - - - -
55C HIS* 5.6 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 33 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C ILE* 3.6 26.4 - - + +
9C GLU* 4.3 7.4 - - + -
10C LEU* 3.7 35.9 - - + -
13C LEU* 4.0 22.0 - - + -
23C ALA* 4.1 7.9 - - + -
24C GLY 3.1 27.8 - - - +
25C PRO* 3.7 15.3 - - + +
26C VAL* 3.7 4.9 - - - -
30C MET* 2.9 26.1 + - + +
32C HIS* 1.3 89.0 - - - +
34C GLN* 1.3 60.4 + - - +
35C ALA 4.1 0.2 + - - -
53C THR* 3.4 5.7 - - - -
54C ILE* 2.9 50.5 + - + +
56C PHE* 3.4 27.3 - + - -
99C ILE* 4.3 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 34 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C ALA* 3.1 20.9 - - - -
24C GLY 3.0 12.7 + - - +
26C VAL* 3.5 20.0 - - + +
32C HIS* 5.1 1.1 - - + +
33C TRP* 1.3 74.5 - - - +
35C ALA* 1.3 60.8 + - - +
36C THR* 5.3 0.8 + - - -
51C PHE* 3.5 34.8 - - + +
52C LEU 3.4 8.1 - - - +
53C THR* 4.8 10.1 - - + +
70C THR* 5.5 7.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 35 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C SER 3.0 6.5 - - - +
23C ALA* 3.2 20.9 - - + +
34C GLN* 1.3 74.5 - - - +
36C THR* 1.3 62.7 + - - +
51C PHE* 3.1 7.9 - - - +
52C LEU* 2.7 46.0 + - + +
54C ILE* 3.7 18.4 - - + -
103C LEU* 4.1 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 36 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C CYS* 2.8 30.8 - - - +
22C SER* 2.6 26.9 + - - +
34C GLN 5.3 1.0 + - - -
35C ALA* 1.3 75.8 - - - +
37C ILE* 1.3 65.9 + - - +
38C MET* 4.2 17.5 - - + -
49C VAL* 3.8 27.1 - - + -
50C PHE 3.4 3.1 - - - +
51C PHE* 4.4 18.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 37 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C GLN 3.3 2.9 - - - -
21C CYS* 3.7 12.8 - - + -
36C THR* 1.3 79.4 - - - +
38C MET* 1.3 73.7 + - - +
50C PHE* 2.6 50.2 + - + +
52C LEU* 3.5 34.5 - - + -
69C PHE* 4.0 9.6 - - + -
103C LEU* 4.2 9.6 - - + +
106C ILE* 4.0 20.2 - - + -
107C CYS* 4.1 13.9 - - - -
110C LEU* 3.8 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 38 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C GLN* 2.4 60.5 + - + +
21C CYS* 5.4 0.4 - - - -
36C THR* 4.2 21.3 - - + -
37C ILE* 1.3 81.0 - - - +
39C GLY* 1.3 65.9 + - - +
40C PRO* 3.1 10.2 - - - +
48C GLY 3.4 8.7 - - - +
49C VAL* 3.9 23.3 - - + -
107C CYS* 4.9 0.3 - - - -
----------------------------------------------------------
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