Contacts of the strand formed by residues 82 - 88 (chain K) in PDB entry 1S5E
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 82 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20K LEU* 4.3 5.2 - - + -
21K ASN* 2.9 27.0 + - - -
22K ASP 2.9 16.8 + - - +
24K ILE* 3.9 19.7 - - + -
40K ILE* 6.1 0.2 - - + -
42K PHE* 3.7 30.1 - - + -
75K ALA* 5.4 1.8 - - + -
80K ALA 4.1 5.6 - - - +
81K LYS* 1.3 74.3 - - - +
83K GLU* 1.3 60.1 + - - +
84K LYS 4.0 22.7 - - - +
85K LEU* 4.3 5.8 - - + -
99K ILE* 4.0 23.6 - - + -
100K SER 3.8 4.0 - - - +
101K MET* 4.2 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 83 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5K ILE* 4.7 2.1 - - - +
19K THR* 3.8 1.0 - - - +
20K LEU 2.9 26.7 + - - -
21K ASN* 3.1 27.2 + - - +
81K LYS 3.7 3.4 + - - -
82K VAL* 1.3 72.0 - - - +
84K LYS* 1.3 82.8 + - + +
100K SER* 2.5 44.1 + - - +
102K ALA* 4.3 28.1 - - + +
25L PHE* 6.1 0.2 - - - -
26L SER* 5.8 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 84 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5K ILE* 3.7 27.3 - - + +
6K THR* 4.2 11.9 + - - +
17K ILE* 3.8 18.3 - - + +
18K HIS 3.3 6.1 - - - +
19K THR* 2.9 40.1 + - + +
20K LEU 4.7 0.2 - - - +
82K VAL* 4.0 2.4 - - - +
83K GLU* 1.3 105.0 - - + +
85K LEU* 1.3 66.2 + - - +
99K ILE* 3.6 3.6 - - - +
100K SER* 3.0 34.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 85 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5K ILE* 4.2 2.2 - - - -
16K GLN 3.8 0.5 - - - +
17K ILE* 3.4 6.4 - - - +
18K HIS* 2.9 35.3 + - + +
20K LEU* 3.9 11.0 - - + +
40K ILE* 4.2 9.0 - - + -
42K PHE* 4.1 13.2 - - + -
48K PHE* 3.4 43.7 - - + -
82K VAL* 4.3 4.0 - - + -
84K LYS* 1.3 73.4 - - - +
86K CYS* 1.3 58.6 + - - +
87K VAL* 4.0 12.4 + - + +
96K ILE* 4.3 17.7 - - + -
98K ALA 3.5 6.1 - - - +
99K ILE* 3.7 39.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 86 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5K ILE* 3.7 15.1 - - + +
8K LEU* 5.2 2.7 - - + -
9K CYS* 2.1 52.7 - - + -
12K TYR* 5.7 2.2 - - - -
15K THR* 4.1 7.9 - - - -
16K GLN 3.6 4.3 - - - -
17K ILE* 4.0 2.0 - - + -
85K LEU* 1.3 72.1 - - - +
87K VAL* 1.3 62.0 + - - +
96K ILE* 3.8 0.5 - - - -
97K ALA* 2.8 37.2 + - - -
98K ALA* 2.9 29.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 87 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15K THR* 3.0 32.0 - - - -
16K GLN* 3.0 21.9 + - + +
18K HIS* 3.5 17.9 - - + +
48K PHE* 3.8 30.1 - - + -
85K LEU* 4.1 11.2 - - + -
86K CYS* 1.3 79.7 - - - +
88K TRP* 1.3 60.8 + - - +
94K HIS* 3.4 34.8 - - + +
95K ALA 3.1 12.8 - - - +
96K ILE* 4.3 6.3 - - - -
97K ALA* 4.2 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 88 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12K TYR* 4.5 14.0 - + - +
13K HIS 3.7 14.1 + - - -
14K ASN* 3.2 8.7 - - + -
15K THR* 3.6 22.0 - - + +
51K GLU* 4.6 11.9 - - - +
57K HIS* 6.0 2.9 - + - -
61K GLN* 4.3 11.2 - - - -
87K VAL* 1.3 72.6 - - - +
89K ASN* 1.3 58.8 + - - +
90K ASN* 3.4 21.2 + - - +
91K LYS* 4.2 6.2 + - + -
94K HIS* 3.5 6.1 - - - -
95K ALA* 2.8 56.8 + - + +
96K ILE 3.6 12.8 - - - -
97K ALA* 3.5 27.8 - - + -
31L LEU* 3.7 15.9 - - + -
32L ALA* 4.1 17.5 - - + -
33L GLY 5.1 0.9 - - - -
----------------------------------------------------------
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