Contacts of the strand formed by residues 21 - 31 (chain T) in PDB entry 4C4K
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 VAL 21 (chain T).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9O ALA* 3.6 32.0 - - + +
88O ILE* 3.1 20.5 + - + +
89O GLY* 3.2 0.5 - - - -
90O GLU 2.9 27.4 + - - +
16T ILE* 3.9 3.1 - - - +
20T LYS* 1.3 76.9 - - - +
22T LEU* 1.3 62.8 + - - +
23T THR* 4.1 17.5 - - + -
65T ILE* 4.3 2.9 - - + -
66T ILE 3.5 9.4 - - - +
67T MET* 4.2 31.4 - - + +
68T ASP 4.3 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 22 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90O GLU 3.5 2.9 - - - +
92O PHE* 3.6 36.3 - - + -
14T ILE* 4.3 6.3 - - + -
16T ILE* 4.0 26.5 - - + -
20T LYS 4.1 0.2 + - - -
21T VAL* 1.3 73.0 - - - +
23T THR* 1.3 75.1 + - - +
24T VAL* 3.5 24.5 - - + -
64T LEU* 5.0 1.8 - - + +
65T ILE* 3.4 0.9 - - - +
66T ILE* 2.8 48.9 + - + +
69T VAL* 3.9 19.5 - - + -
94T ILE* 4.1 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 23 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9O ALA* 5.4 1.1 - - + -
10O PRO 3.6 14.5 + - - +
11O ARG* 4.9 4.5 - - + -
12O PHE* 5.2 2.1 + - - -
90O GLU 3.0 8.6 + - - +
91O ALA* 3.0 26.5 - - - +
92O PHE 2.9 25.4 + - - -
21T VAL* 4.1 11.0 - - + -
22T LEU* 1.3 82.2 - - - +
24T VAL* 1.3 66.2 + - - +
25T ALA* 4.2 0.6 - - - +
63T THR* 4.2 9.5 - - + +
64T LEU 3.3 6.7 - - - -
65T ILE* 3.6 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 24 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92O PHE* 3.4 9.0 - - + +
10T LEU* 3.9 28.7 - - + -
11T PRO* 4.6 9.0 - - + -
14T ILE* 3.0 36.8 - - + -
22T LEU* 3.5 15.0 - - + -
23T THR* 1.3 78.5 - - - +
25T ALA* 1.3 64.3 + - - +
38T TRP* 4.5 8.6 - - + -
62T THR 3.9 0.9 - - - +
63T THR* 3.4 3.0 - - - -
64T LEU* 2.9 43.5 + - + +
92T VAL* 5.0 4.0 - - + -
94T ILE* 4.6 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 25 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12O PHE* 4.4 19.5 - - + -
16O PRO* 5.6 0.6 - - + +
92O PHE 2.9 11.6 + - - +
93O ALA* 3.5 29.8 - - + +
94O ALA 4.3 3.8 + - - +
9T ALA 4.9 1.2 - - - +
10T LEU* 5.1 1.0 - - - +
11T PRO* 5.6 0.9 - - - +
23T THR* 4.2 0.8 - - - +
24T VAL* 1.3 76.4 - - - +
26T CYS* 1.3 62.6 + - - +
61T LEU* 4.1 15.0 - - + -
62T THR 3.4 4.5 - - - -
63T THR* 3.8 19.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 26 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16O PRO* 6.2 0.7 - - - -
94O ALA 6.0 0.7 - - - -
7T ILE* 3.3 29.4 - - - -
9T ALA 3.3 24.2 - - - -
10T LEU* 4.1 15.5 - - + -
25T ALA* 1.3 76.0 - - - +
27T ALA* 1.3 68.3 + - - +
28T PHE* 3.9 0.7 - - - -
38T TRP* 4.9 3.4 - - + -
61T LEU* 3.5 5.4 - - - +
62T THR* 2.9 40.8 + - + +
79T LEU* 3.6 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 27 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15O ARG* 3.6 47.1 - - + +
16O PRO* 5.2 5.4 - - + +
94O ALA 5.6 2.2 + - - +
7T ILE 3.8 0.2 - - - -
8T GLU* 2.9 34.4 + - + +
9T ALA 5.0 1.0 + - - -
26T CYS* 1.3 82.4 - - - +
28T PHE* 1.3 63.4 + - - +
60T ASP 3.2 12.8 - - - +
61T LEU* 3.8 3.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 28 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15O ARG* 5.1 2.3 + - - -
6T LYS 3.3 7.9 - - - +
7T ILE* 4.4 0.9 - - + -
8T GLU* 4.3 2.5 - - - +
26T CYS* 3.9 7.4 - - - -
27T ALA* 1.3 80.7 - - - +
29T THR* 1.3 69.7 + - - +
33T THR* 4.4 0.9 - - + -
34T PRO* 3.7 34.8 - - + -
36T VAL* 3.7 19.3 - - + -
58T THR 3.6 9.4 - - - -
59T ASP 3.3 19.9 - - - +
60T ASP* 3.0 23.1 + - - +
61T LEU 3.5 26.2 - - - -
62T THR* 3.7 9.4 - - + -
79T LEU* 5.5 0.9 - - + -
81T LEU* 3.4 29.6 - - + -
1102T EDO 3.6 23.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 29 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15O ARG* 5.0 11.4 - - - +
3T ILE* 5.3 5.5 - - - +
4T PRO 4.6 1.4 + - - -
5T PRO* 3.2 6.6 - - - +
6T LYS* 3.0 45.3 + - - +
28T PHE* 1.3 84.0 - - - +
30T GLY* 1.3 59.9 + - - +
34T PRO* 4.1 5.4 - - - +
60T ASP* 6.0 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 30 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3T ILE* 3.5 17.0 - - - +
4T PRO 3.8 7.0 - - - -
5T PRO* 4.0 4.5 - - - -
29T THR* 1.3 78.4 - - - +
31T GLU* 1.3 75.1 + - - +
32T PRO 3.1 16.1 - - - +
33T THR* 3.7 6.1 + - - -
34T PRO* 3.9 3.7 - - - +
83T ASN* 4.1 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 31 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2T GLY* 4.1 4.0 + - - +
3T ILE* 2.9 58.3 + - + +
30T GLY* 1.3 82.4 + - - +
32T PRO* 1.4 70.1 + - - +
33T THR* 4.9 4.5 + - - -
83T ASN* 3.5 2.0 - - - -
85T PHE* 3.3 12.0 - - - -
----------------------------------------------------------
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