Contacts of the strand formed by residues 100 - 105 (chain K) in PDB entry 5LN3
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 THR 100 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96K VAL* 2.9 16.0 + - - +
97K ASP* 2.8 54.3 + - - +
98K GLN 3.9 3.6 - - - +
99K ASN* 1.3 87.3 - - + +
101K ALA* 1.3 62.8 + - - +
112K TYR* 3.2 30.2 + - + +
113K VAL 3.4 3.8 - - - -
114K ARG* 3.8 16.2 - - - +
121K ARG* 3.4 6.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 101 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92K PHE* 3.8 22.7 - - + -
94K GLU 3.5 13.9 - - - +
96K VAL* 3.7 8.7 - - - +
100K THR* 1.3 78.1 - - - +
102K ILE* 1.4 58.7 + - - +
103K VAL* 4.1 3.8 - - + -
112K TYR* 3.1 6.1 - - - -
113K VAL* 2.8 46.0 + - + +
115K ILE* 5.1 5.8 - - + -
121K ARG* 4.4 4.9 - - - +
139K LEU* 6.2 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 102 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73J VAL* 4.0 31.6 - - + -
113J ARG* 4.1 27.1 - - - +
127J LEU* 4.3 6.3 - - + -
93K LEU* 3.1 27.1 + - + -
94K GLU* 3.0 56.7 + - + +
96K VAL* 3.6 17.2 - - + +
101K ALA* 1.4 72.1 - - - +
103K VAL* 1.4 63.9 + - - +
110K ASN* 5.2 0.9 - - + -
111K TYR 3.6 11.2 - - - +
112K TYR* 4.5 2.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 103 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90K GLY* 4.5 1.8 - - - -
91K GLN 3.2 23.8 - - - +
92K PHE* 3.9 23.3 - - + +
93K LEU* 3.6 8.1 - - - +
101K ALA* 4.1 3.1 - - + -
102K ILE* 1.4 80.0 - - - +
104K GLY* 1.4 67.7 + - - +
105K SER* 4.1 2.9 - - - +
110K ASN* 3.5 4.9 - - - +
111K TYR* 2.9 32.7 + - + +
113K VAL* 3.8 22.4 - - + -
132K LEU* 4.0 34.5 - - + -
139K LEU* 5.1 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 104 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91K GLN* 2.9 32.9 + - - +
93K LEU* 3.5 18.2 - - - +
103K VAL* 1.4 76.2 - - - +
105K SER* 1.3 66.1 + - - -
106K THR* 4.6 0.3 - - - +
108K GLY 6.2 0.2 - - - -
109K SER 4.8 0.2 - - - -
110K ASN* 3.9 10.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 105 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89K ILE 4.7 3.6 - - - -
90K GLY* 3.9 12.4 - - - -
103K VAL* 4.1 5.1 - - - +
104K GLY* 1.3 76.0 - - - +
106K THR* 1.4 54.8 + - - +
107K THR* 3.3 20.9 - - - -
108K GLY* 2.9 24.6 + - - -
109K SER 3.0 22.3 + - - -
111K TYR* 3.8 15.4 - - - -
132K LEU* 4.9 7.4 - - - +
137K ASN* 5.1 2.3 + - - -
----------------------------------------------------------
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