Contacts of the strand formed by residues 108 - 114 (chain B) in PDB entry 4R7P
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 108 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B VAL 4.0 7.4 - - - +
105B LEU* 3.0 20.7 + - + +
106B ASN 3.5 0.2 - - - -
107B LYS* 1.3 81.3 - - - +
109B VAL* 1.3 82.2 + - - +
110B VAL* 4.3 10.1 - - + +
149B LEU* 6.2 0.2 - - + -
157B VAL* 3.9 6.5 - - + +
158B PRO* 3.5 19.4 - - - +
244B LYS* 4.2 4.0 + - - +
246B TYR* 3.5 17.5 - - + +
248B PHE* 3.9 18.2 - - + +
259B VAL* 3.4 34.1 - - + -
264B LEU* 4.2 12.1 - - + -
268B MET* 4.2 3.4 - - + -
333B TRP* 4.0 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 109 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B LEU* 1.3 80.4 - - - +
110B VAL* 1.3 65.4 + - - +
111B VAL* 3.7 1.7 + - + -
158B PRO* 3.7 23.3 - - + +
160B VAL* 3.7 29.6 - - + -
230B PHE* 5.1 0.2 - - + -
239B PHE* 3.9 17.9 - - + -
244B LYS* 3.7 28.7 - - + -
246B TYR 2.8 10.5 + - - +
247B ILE* 3.2 24.7 - - + +
248B PHE 2.8 26.3 + - - -
336B LEU* 4.9 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 110 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B LEU* 4.7 11.4 - - + -
109B VAL* 1.3 71.7 - - - +
111B VAL* 1.3 62.4 + - - +
112B LYS* 4.5 18.2 - - - -
142B THR* 5.2 0.2 - - + -
146B ILE* 3.7 35.4 - - + -
149B LEU* 6.1 0.2 - - + -
157B VAL* 3.7 20.2 - - + -
158B PRO 3.2 7.9 + - - +
159B LEU* 3.6 8.3 - - + +
160B VAL* 2.8 29.3 + - - +
248B PHE* 3.9 22.7 - - + +
250B SER* 5.4 0.2 - - - +
259B VAL* 5.2 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 111 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B VAL* 4.2 2.7 - - + +
110B VAL* 1.3 76.3 - - - +
112B LYS* 1.3 67.7 + - - +
113B LEU* 4.9 0.4 - - + +
160B VAL* 3.5 26.7 - - + +
162B MET* 4.8 7.9 - - + -
188B PHE* 4.8 2.2 - - + -
226B ILE* 3.9 26.0 - - + -
230B PHE* 5.0 5.8 - - + -
247B ILE* 3.7 37.2 - - + -
248B PHE 2.8 15.0 + - - +
249B VAL* 3.2 10.5 - - + +
250B SER* 2.9 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 112 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B VAL* 4.5 9.4 - - + -
111B VAL* 1.3 75.6 - - - +
113B LEU* 1.3 63.0 + - - +
114B ASN* 3.3 1.8 + - + +
142B THR* 3.5 41.0 + - + -
145B GLN* 5.2 3.9 + - - -
159B LEU* 3.9 9.4 - - + -
160B VAL 3.1 6.5 + - - -
161B LEU* 3.6 18.5 - - + -
162B MET 3.0 24.9 + - - -
248B PHE* 5.1 1.4 - - - -
250B SER* 3.0 26.8 + - - +
251B ASN 4.0 15.7 + - - +
252B ILE* 4.0 20.4 + - + +
254B ASN 4.5 4.2 + - - -
257B ALA* 3.1 28.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 113 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B VAL* 4.0 0.9 + - + -
112B LYS* 1.3 70.5 - - - +
114B ASN* 1.3 57.6 + - - +
115B GLY 3.7 3.5 + - - +
162B MET* 3.8 33.9 - - + -
223B HIS* 4.1 31.6 - - + -
226B ILE* 4.3 9.0 - - + -
249B VAL* 4.1 24.5 - - + -
250B SER* 2.8 18.8 + - - +
251B ASN* 3.6 27.6 - - - +
252B ILE* 3.2 26.3 + - - +
330B ASN* 4.6 8.7 - - - +
372B VAL* 5.2 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B LYS 3.3 6.5 + - - +
113B LEU* 1.3 72.8 - - - +
115B GLY* 1.3 58.0 + - - +
116B GLY 3.6 3.6 - - - +
126B PRO* 4.6 5.5 - - - +
128B SER* 2.8 35.7 + - - -
139B LEU* 5.6 1.6 - - - +
161B LEU* 4.4 15.0 - - + +
162B MET 2.7 22.8 + - - +
163B ASN* 3.1 19.0 + - - +
167B THR* 2.8 19.2 + - - -
171B THR* 3.4 27.8 + - - +
252B ILE* 4.3 7.1 - - + +
----------------------------------------------------------
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