Contacts of the strand formed by residues 23 - 30 (chain H) in PDB entry 6A5T
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 23 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538A ARG* 4.4 30.3 - - + +
539A ASP* 4.6 3.3 - - - +
541A PHE* 3.7 33.9 - - + -
17H ASN* 4.4 5.2 - - - +
20H TYR* 3.4 31.2 - - + +
21H ASN 3.9 0.2 - - - -
22H LYS* 1.3 82.7 - - + +
24H SER* 1.3 61.4 + - - +
41H ASP* 3.7 28.3 - - + -
42H ILE 2.9 17.7 - - - +
43H ASN* 4.4 1.1 - - + -
44H ASN* 3.6 1.1 - - - -
120H LEU* 5.0 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 24 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15H VAL* 3.6 16.1 - - - +
16H ASP 3.4 10.1 - - - -
17H ASN* 3.1 28.9 - - - -
23H VAL* 1.3 73.7 - - - +
25H ARG* 1.3 59.8 + - - +
41H ASP* 3.4 3.0 - - - -
42H ILE* 2.6 64.6 + - - +
44H ASN* 2.9 9.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 25 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538A ARG* 3.6 16.8 - - - +
599A LEU* 3.5 37.8 + - - +
600A SER 4.3 0.4 + - - -
601A PRO* 3.9 22.3 - - - +
14H THR 3.6 1.2 - - - +
15H VAL* 3.2 7.3 - - - +
16H ASP* 3.1 35.7 + - + +
24H SER* 1.3 72.3 - - - +
26H ILE* 1.3 65.5 + - - +
27H ILE* 5.0 6.7 - - + +
39H THR* 3.6 23.0 - - + +
40H LEU 3.4 0.7 - - - +
41H ASP* 2.6 43.7 + - - +
121H LEU* 3.9 17.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 26 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12H VAL* 4.4 10.3 - - + -
14H THR 3.6 4.0 - - - -
15H VAL* 3.5 24.2 - - + -
25H ARG* 1.3 75.1 - - - +
27H ILE* 1.3 63.2 + - - +
28H GLY* 5.0 5.4 - - - +
38H LEU* 6.0 4.7 - - + -
39H THR* 3.2 8.0 - - - +
40H LEU* 2.8 65.8 + - + +
42H ILE* 3.9 28.0 - - + -
49H VAL* 4.3 11.0 - - + -
55H LEU* 3.8 28.3 - - + -
143H ILE* 5.4 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 27 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12H VAL* 3.7 2.4 - - - +
13H GLN* 3.0 42.0 + - + +
14H THR* 3.1 35.2 + - - +
25H ARG* 5.0 7.0 - - + +
26H ILE* 1.3 77.6 - - - +
28H GLY* 1.3 62.2 + - - +
29H ILE* 5.1 2.7 - - + -
37H LYS* 4.7 14.8 - - + -
38H LEU 3.3 9.0 - - - +
39H THR* 4.1 14.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 28 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10H PHE* 3.8 13.7 - - - -
11H THR 3.4 10.3 - - - -
12H VAL* 4.5 5.6 - - - -
26H ILE* 3.9 5.6 + - - +
27H ILE* 1.3 74.0 - - - +
29H ILE* 1.3 65.2 + - - +
37H LYS* 3.8 0.9 - - - +
38H LEU* 2.8 45.0 + - - +
55H LEU* 6.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 29 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10H PHE* 3.3 4.9 - - - -
11H THR* 2.9 34.6 + - - +
13H GLN* 3.1 42.0 - - - +
27H ILE* 4.1 4.4 + - + -
28H GLY* 1.3 79.3 - - - +
30H SER* 1.3 76.7 + - - +
34H SER* 4.6 19.3 - - - -
35H ALA 5.5 1.1 - - - +
36H ILE 4.1 4.5 - - - +
37H LYS* 4.6 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 30 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8H ASP* 2.7 26.6 + - - -
9H ILE 3.5 8.3 - - - -
10H PHE* 3.4 10.2 - - - -
29H ILE* 1.3 93.7 - - - +
31H THR* 1.3 72.8 + - - +
32H THR* 3.1 19.8 + - - -
33H ASN 3.1 24.9 + - - +
34H SER* 4.8 1.9 + - - -
36H ILE* 3.9 9.9 + - - +
----------------------------------------------------------
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