Contacts of the strand formed by residues 31 - 35 (chain K) 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 ILE 31 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21K ILE* 4.3 16.4 - - + -
22K THR 3.9 4.0 - - - +
23K PRO* 4.0 16.6 - - + -
24K ASP* 3.6 7.2 - - - +
29K ASN 5.5 0.2 - - - -
30K CYS* 1.3 82.5 - - - +
32K ILE* 1.3 68.8 + - - +
33K ILE* 3.5 25.1 - - + -
74K ARG* 3.2 6.1 - - - +
75K LEU* 2.9 47.0 + - + +
83K PRO* 4.1 27.4 - - + -
84K LYS* 5.0 5.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 32 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552A PHE* 4.4 8.5 - - + -
21K ILE* 3.5 3.6 - - - +
22K THR* 2.9 51.5 + - - +
23K PRO 5.3 0.2 - - - -
24K ASP* 4.2 14.4 - - + +
26K ARG* 5.4 1.8 - - - +
31K ILE* 1.3 85.9 - - - +
33K ILE* 1.3 75.2 + - - +
34K LYS* 4.9 1.6 - - + +
72K VAL* 3.4 25.1 - - + -
73K MET 3.3 2.2 - - - +
74K ARG* 3.4 35.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 33 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262C LEU* 5.5 1.6 - - + -
19K LEU* 3.5 35.0 - - + -
20K LYS 3.5 3.4 - - - +
21K ILE* 4.2 16.6 - - + -
31K ILE* 3.5 27.6 - - + -
32K ILE* 1.3 82.1 - - - +
34K LYS* 1.3 62.8 + - - +
35K PHE* 3.7 26.3 + - + -
72K VAL* 3.2 9.1 - - - +
73K MET* 2.8 44.3 + - + +
75K LEU* 5.0 8.5 - - + -
87K LEU* 4.8 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 34 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18K LYS 4.8 0.2 - - - -
19K LEU* 3.4 4.7 - - - -
20K LYS* 2.8 49.6 + - + +
22K THR* 5.8 2.2 + - + -
32K ILE* 4.3 1.7 - - + +
33K ILE* 1.3 72.3 - - - +
35K PHE* 1.3 63.4 + - - +
36K GLU* 4.4 11.3 + - + +
64K GLU* 4.6 17.5 + - - +
70K ASN* 3.1 40.4 - - - +
71K PHE 3.6 13.5 - - - +
72K VAL* 4.5 10.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 35 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258C VAL* 4.5 10.1 - - + -
18K LYS* 4.2 5.4 - - - -
19K LEU* 3.4 27.1 - - + +
33K ILE* 3.7 22.7 - - + -
34K LYS* 1.3 78.9 - - - +
36K GLU* 1.3 70.1 + - - +
38K GLU* 4.2 15.5 - - + -
42K LEU* 3.9 17.7 - - + -
46K LEU* 4.2 20.6 - - + -
70K ASN* 3.4 18.0 - - - +
71K PHE* 3.0 60.2 + + + +
73K MET* 4.4 18.8 - - + -
87K LEU* 5.8 4.9 - - + -
----------------------------------------------------------
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