Contacts of the strand formed by residues 109 - 118 (chain B) in PDB entry 4LKC
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 ASN 109 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B TYR* 3.1 30.3 + - + +
103B HIS 3.3 2.9 - - - +
104B ASP* 3.1 37.9 + - - +
105B SER 3.4 2.4 + - - -
106B GLY 3.3 19.0 + - - +
107B SER 4.4 1.0 - - - +
108B ASP* 1.3 94.7 + - - +
110B TYR* 1.3 62.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 110 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A SER* 4.1 7.8 + - - -
51A ASP* 2.7 41.4 + - - -
102B TYR* 3.3 13.3 - - - -
103B HIS* 2.8 70.0 + + + +
108B ASP* 4.2 16.6 - - + +
109B ASN* 1.3 77.4 - - - +
111B TYR* 1.3 74.6 + - - +
112B SER* 4.5 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 111 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B THR* 4.9 13.2 - - + -
101B TYR 3.3 9.9 - - - -
102B TYR* 3.5 46.3 - + + -
110B TYR* 1.3 87.7 - - - +
112B SER* 1.3 60.8 + - - +
113B TYR* 3.6 33.0 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 112 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A TYR* 3.2 26.0 - - - -
51A ASP* 3.5 36.5 - - - +
100B THR* 3.6 0.2 - - - -
101B TYR* 2.7 39.3 + - - +
103B HIS* 5.2 2.4 + - - +
110B TYR* 4.2 3.3 + - - -
111B TYR* 1.3 72.0 - - - +
113B TYR* 1.4 75.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 113 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ALA* 4.5 2.1 - - - +
50A TYR* 3.5 16.8 - - - +
51A ASP 4.4 3.0 + - - +
92A PHE* 3.4 53.3 - + + +
98B GLU* 3.4 22.9 - - - +
99B GLY 3.5 12.3 - - - +
100B THR* 3.7 21.3 - - + -
101B TYR* 4.0 6.1 - - - -
111B TYR* 3.6 35.8 - + + +
112B SER* 1.4 81.9 - - - +
114B GLY* 1.3 59.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A TYR* 4.1 2.0 - - - -
47A LEU* 4.0 21.3 - - - -
92A PHE* 3.6 12.8 - - - -
98B GLU* 3.5 2.6 - - - -
99B GLY* 2.7 37.8 + - - -
101B TYR* 3.7 4.3 - - - -
113B TYR* 1.3 78.0 - - - +
115B MET* 1.3 59.6 + - - -
116B ASP* 3.2 3.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A TYR* 2.9 31.6 + - + +
47A LEU* 3.5 6.0 - - - +
90A GLN* 4.0 10.8 - - - +
92A PHE* 4.0 7.6 - - + -
97A ILE* 3.8 44.2 - - + -
99A PHE* 3.9 15.5 - - + -
35B HIS* 4.2 19.7 - - + +
37B VAL* 4.1 10.8 - - + -
47B TRP* 4.4 1.1 - - + -
96B VAL* 3.5 24.2 - - + -
97B ARG 3.4 8.1 - - - +
98B GLU* 5.3 0.4 - - - -
114B GLY* 1.3 67.7 - - - -
116B ASP* 1.3 58.9 + - - +
117B VAL 3.6 2.9 - - - -
118B TRP* 2.9 44.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A LEU* 4.0 12.0 + - + +
56A GLU* 3.8 15.2 - - - +
97B ARG* 2.8 50.2 + - - +
99B GLY* 3.7 18.0 + - - -
101B TYR* 3.4 25.1 + - - +
114B GLY 3.2 2.2 + - - +
115B MET* 1.3 73.5 - - - +
117B VAL* 1.3 70.6 + - + +
118B TRP* 4.4 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 117 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B VAL* 3.6 36.8 - - + +
3B GLN* 4.8 2.9 - - - -
4B LEU* 3.3 21.1 - - + +
96B VAL* 3.4 4.5 - - - +
97B ARG* 2.8 58.7 + - + +
115B MET 3.6 0.2 - - - -
116B ASP* 1.3 96.7 + - - +
118B TRP* 1.3 70.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 118 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A TYR* 4.1 15.3 - + - -
44A ALA* 3.7 18.5 - - + +
45A PRO* 3.4 53.7 + - + +
46A LYS* 5.3 1.3 - - - -
47A LEU 5.4 0.2 - - - -
99A PHE* 4.1 13.7 - + - -
4B LEU* 4.2 5.0 + - - +
37B VAL* 3.7 35.9 - - + -
45B LEU* 4.3 5.4 - - + -
94B TYR* 3.9 14.4 - + + -
95B CYS 3.5 5.2 - - - -
96B VAL* 3.5 18.2 - - + -
115B MET* 2.9 48.5 + - + +
116B ASP 4.4 2.0 - - - -
117B VAL* 1.3 87.5 - - - +
119B GLY* 1.3 63.1 + - - +
----------------------------------------------------------
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