Contacts of the strand formed by residues 108 - 114 (chain A) 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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A VAL 3.5 8.0 + - - +
105A LEU* 3.2 22.7 + - + +
106A ASN 3.4 0.2 - - - -
107A LYS* 1.3 80.6 - - - +
109A VAL* 1.3 79.5 + - - +
110A VAL* 4.6 9.6 - - + +
157A VAL* 4.0 5.7 - - + +
158A PRO* 3.6 15.8 - - - +
244A LYS* 4.0 6.6 + - - -
246A TYR* 3.5 18.2 - - + +
248A PHE* 3.9 18.8 - - + +
259A VAL* 3.4 33.9 - - + -
264A LEU* 4.2 11.7 - - + -
268A MET* 4.0 6.1 - - + -
333A TRP* 4.2 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A LEU* 1.3 77.3 - - - +
110A VAL* 1.3 73.2 + - - +
111A VAL* 3.6 1.3 + - + -
157A VAL* 4.6 0.2 - - - -
158A PRO* 3.5 26.7 - - + -
160A VAL* 4.0 17.7 - - + -
239A PHE* 4.3 12.3 - - + -
244A LYS* 4.3 11.0 - - + -
246A TYR 2.8 19.6 + - - +
247A ILE* 3.1 31.0 - - + -
248A PHE 2.9 25.9 + - - -
336A LEU* 4.1 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A LEU* 4.8 10.8 - - + -
109A VAL* 1.3 74.2 - - - +
111A VAL* 1.3 64.6 - - - +
112A LYS* 4.2 22.0 - - + +
146A ILE* 3.7 33.0 - - + -
149A LEU* 6.2 0.2 - - + -
157A VAL* 3.9 16.4 - - + -
158A PRO 3.4 11.1 + - - +
159A LEU* 3.6 10.9 - - + -
160A VAL* 2.8 26.5 + - - +
248A PHE* 3.9 18.6 - - + +
259A VAL* 5.1 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A VAL* 3.6 2.7 + - + -
110A VAL* 1.3 79.2 - - - +
112A LYS* 1.3 76.4 + - - +
113A LEU* 4.5 3.1 - - + -
160A VAL* 3.3 23.8 - - + +
162A MET* 4.8 0.4 - - + -
188A PHE* 4.6 11.2 - - + -
226A ILE* 4.2 15.0 - - + -
230A PHE* 4.6 7.2 - - + -
247A ILE* 3.8 34.1 - - + -
248A PHE 2.9 18.8 + - - +
249A VAL* 3.7 22.9 - - + -
250A SER 3.2 15.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A VAL* 4.2 9.4 - - + +
111A VAL* 1.3 77.4 - - - +
113A LEU* 1.3 64.0 + - - +
114A ASN* 3.5 0.5 + - - +
142A THR* 3.6 30.3 - - + -
145A GLN* 5.0 4.8 + - - -
159A LEU* 3.8 18.6 - - + -
160A VAL 2.8 7.1 + - - -
161A LEU* 3.6 18.1 - - + -
162A MET* 2.9 27.2 + - - +
248A PHE* 4.8 2.4 - - - -
250A SER* 2.7 30.5 + - - +
251A ASN 4.0 15.8 + - - +
252A ILE* 4.2 16.2 - - + -
254A ASN 4.9 2.0 + - - -
257A ALA* 3.1 25.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A VAL* 4.5 5.6 - - + -
112A LYS* 1.3 77.0 - - - +
114A ASN* 1.3 58.5 + - - +
115A GLY 3.7 3.4 - - - +
162A MET* 4.2 24.7 - - + -
223A HIS* 3.5 44.4 - - + +
226A ILE* 4.5 13.2 - - + -
249A VAL* 4.8 8.5 - - + -
250A SER 2.9 21.1 + - - +
251A ASN* 3.4 22.2 - - - +
252A ILE* 3.6 25.5 + - - +
330A ASN* 5.6 3.4 - - - +
372A VAL* 5.5 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A LYS 3.5 2.9 + - - +
113A LEU* 1.3 73.2 - - - +
115A GLY* 1.3 58.6 + - - +
116A GLY 3.2 14.5 + - - -
126A PRO* 4.4 7.3 - - - +
127A LYS* 5.8 0.2 - - - +
128A SER* 2.4 36.4 + - - -
139A LEU* 5.3 0.2 - - - +
161A LEU* 4.1 14.7 - - + +
162A MET 2.8 16.6 + - - +
163A ASN* 3.2 24.9 - - - +
167A THR* 2.9 20.1 + - - -
171A THR* 4.0 13.9 - - - +
252A ILE* 4.8 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