Contacts of the strand formed by residues 91 - 99 (chain B) in PDB entry 5LK5
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 LEU 91 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B TYR* 5.1 0.2 - - + -
84B PHE* 3.6 34.5 - - + -
86B ASN* 4.0 20.0 - - + +
89B GLN 3.7 0.6 + - - -
90B THR* 1.3 74.4 - - - +
92B VAL* 1.3 66.3 + - - +
93B VAL* 4.3 8.7 - - + -
112B LEU* 4.1 9.4 - - + -
130B ILE* 3.9 28.3 - - + -
174B LEU 3.7 1.0 - - - +
175B ILE* 3.5 2.3 - - - -
176B VAL* 2.8 50.0 + - + +
311B PHE* 3.9 18.6 - - + -
332B ILE* 3.8 16.6 - - + -
333B THR 3.8 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 92 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B THR* 4.0 17.5 - - + -
91B LEU* 1.3 79.1 - - - +
93B VAL* 1.3 66.4 + - - +
94B GLN* 4.7 2.5 - - + -
173B THR* 3.8 17.5 - - + -
174B LEU 3.3 9.6 - - - +
175B ILE* 4.2 8.7 - - + -
331B LEU 3.6 0.9 - - - +
332B ILE* 3.3 9.2 - - - +
333B THR* 2.8 48.7 + - + +
335B ASP 4.1 4.7 - - - +
336B GLU* 4.0 24.7 - - - +
339B ALA* 3.6 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 93 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B LEU* 4.3 13.2 - - + -
92B VAL* 1.3 74.8 - - - +
94B GLN* 1.3 64.6 + - - +
95B PHE* 4.8 3.1 - - + -
110B VAL* 4.1 26.2 - - + -
112B LEU* 3.4 36.8 - - + -
130B ILE* 5.7 2.0 - - + -
132B PHE* 4.0 11.0 - - + -
172B TYR 3.8 0.7 - - - +
173B THR* 3.4 1.7 - - - +
174B LEU* 2.8 56.7 + - + +
314B LEU* 5.0 3.1 - - + -
331B LEU 3.7 4.5 - - - +
332B ILE* 4.8 8.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 94 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B VAL* 4.7 5.2 - - + -
93B VAL* 1.3 77.3 - - - +
95B PHE* 1.3 70.0 + - - +
171B LEU* 3.7 20.8 - - + +
172B TYR 3.2 13.0 - - - +
173B THR* 2.8 30.6 + - + +
188B ASN* 4.5 2.3 - - - +
329B ASN 4.2 2.2 + - - +
330B PHE* 3.4 1.2 - - - +
331B LEU* 2.8 46.0 + - + +
339B ALA* 3.0 35.0 + - - +
342B PHE* 4.1 15.6 - - - -
343B GLY* 3.6 17.4 - - - +
346B THR* 5.2 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 95 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B VAL* 4.8 1.1 - - + -
94B GLN* 1.3 84.7 - - - +
96B THR* 1.3 66.4 + - - +
97B VAL* 3.3 31.0 - - + -
108B GLY 3.4 14.4 - - - -
110B VAL* 3.7 39.7 - - + -
132B PHE* 3.7 37.7 - + - -
133B GLY* 4.3 7.9 - - - -
134B PRO* 4.6 0.2 - - + -
170B HIS 3.9 0.2 - - - +
171B LEU* 3.7 3.7 - - - +
172B TYR* 2.9 37.1 + - + +
314B LEU* 6.1 0.2 - - + -
327B PHE* 4.5 7.0 - + - -
328B ASP 3.8 4.3 - - - +
329B ASN 3.5 10.1 - - - -
330B PHE* 3.6 22.9 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 96 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B PHE* 1.3 76.7 - - - +
97B VAL* 1.3 65.6 + - - +
169B THR* 3.7 21.9 - - + +
170B HIS 3.3 5.8 - - - +
171B LEU* 3.8 24.0 - - + -
326B ILE 4.4 1.5 + - - -
327B PHE* 3.4 6.6 - - - -
328B ASP* 2.9 55.8 + - - +
329B ASN* 3.5 16.9 + - + +
347B TRP* 4.0 20.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 97 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B PHE* 3.3 35.0 - - + -
96B THR* 1.3 73.1 - - - +
98B LYS* 1.3 62.1 + - - +
99B HIS* 3.8 28.8 + - + +
108B GLY 3.6 9.6 - - - +
134B PRO* 4.2 6.5 - - + -
168B PHE 3.7 2.1 - - - +
169B THR* 4.4 1.1 - - - -
170B HIS* 2.8 41.4 + - - +
172B TYR* 4.1 19.0 - - + -
325B THR* 3.9 16.6 - - + -
326B ILE 3.6 3.4 - - - -
327B PHE* 4.0 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 98 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B SER 3.5 10.1 + - - -
56B PHE* 2.7 39.8 + - - -
57B TYR* 4.4 3.4 - - - +
63B ASP* 5.6 4.2 + - - +
97B VAL* 1.3 75.7 - - - +
99B HIS* 1.3 58.7 + - - +
100B GLU* 3.1 38.3 + - + +
167B GLU 3.5 14.4 - - - +
168B PHE 3.7 6.3 - - - +
169B THR* 3.3 26.2 - - + +
324B GLY 4.0 0.7 - - - +
325B THR* 3.3 2.7 - - - -
326B ILE* 2.9 52.3 + - + +
354B GLU* 3.5 13.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 99 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B VAL* 3.8 17.3 + - + +
98B LYS* 1.3 71.3 - - - +
100B GLU* 1.3 59.8 + - - +
101B GLN* 3.0 15.7 + - - +
102B ASN 3.1 8.8 + - - -
103B ILE* 3.7 39.0 - - + +
106B GLY 4.8 1.5 + - - -
107B GLY 4.3 13.0 - - - -
108B GLY* 4.4 3.3 + - - -
134B PRO* 4.7 10.4 - - + +
136B ILE* 4.0 21.0 - - + +
164B LYS 4.6 7.2 - - - -
165B ASP* 5.3 1.1 - - - +
166B ASP 3.6 13.4 + - - +
167B GLU* 3.4 15.7 + - - -
168B PHE 4.3 4.4 + - - -
325B THR* 2.7 38.6 + - + +
----------------------------------------------------------
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