Contacts of the helix formed by residues 105 - 112 (chain A) in PDB entry 5F2R
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 ASP 105 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ARG* 3.0 37.2 + - - +
102A THR* 3.1 28.1 + - - +
103A TRP 3.2 0.2 - - - -
104A ASN* 1.3 80.3 + - - +
106A PRO* 1.3 76.6 - - - +
107A SER* 2.9 20.6 + - - -
108A VAL* 2.9 20.9 + - + +
109A GLN* 3.0 10.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A ASN 3.2 6.7 - - - +
105A ASP* 1.3 93.1 - - - +
107A SER* 1.3 55.1 + - - +
109A GLN* 3.4 8.6 + - + +
110A GLN* 2.9 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ARG 5.0 0.2 + - - -
101A ARG* 3.7 29.2 + - - -
105A ASP* 2.9 13.1 + - - -
106A PRO* 1.3 76.9 - - - +
108A VAL* 1.3 58.1 + - - +
110A GLN* 3.4 5.7 + - - +
111A ASP* 2.9 42.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ARG 5.6 0.2 - - - -
98A LEU* 4.2 16.2 - - + -
101A ARG* 3.7 31.0 - - + -
102A THR 3.4 16.6 - - - +
103A TRP* 3.5 19.5 - - + +
105A ASP* 2.9 10.5 + - + +
107A SER* 1.3 76.9 - - - +
109A GLN* 1.3 60.6 + - - +
111A ASP* 3.2 5.9 + - - +
112A ILE* 2.9 37.2 + - + +
126A PRO* 3.8 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A TRP* 2.8 63.3 + - - +
104A ASN* 4.4 9.2 - - - +
105A ASP 3.0 11.9 + - - +
106A PRO* 3.4 10.3 + - + +
108A VAL* 1.3 75.0 - - - +
110A GLN* 1.3 62.0 + - - +
112A ILE* 3.6 26.0 - - - +
113A LYS* 3.7 17.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A PRO 2.9 17.6 + - - +
107A SER* 3.7 7.0 - - - +
109A GLN* 1.3 73.8 - - - +
111A ASP* 1.3 67.2 + - - +
113A LYS* 3.2 45.7 + - - +
114A PHE* 3.6 31.1 - - + -
252A HIS* 5.8 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ARG* 3.4 37.3 + - - +
98A LEU* 4.5 11.4 - - + +
107A SER* 2.9 33.9 + - - +
108A VAL* 3.2 6.0 + - - +
110A GLN* 1.3 73.7 - - - +
112A ILE* 1.3 63.6 + - - +
114A PHE* 3.1 17.4 + - - +
115A LEU* 3.4 19.6 + - + +
252A HIS* 2.9 35.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A LEU* 4.6 3.8 - - + -
103A TRP* 3.9 19.7 - - + -
108A VAL* 2.9 27.1 + - + +
109A GLN* 3.6 42.8 - - - +
111A ASP* 1.3 76.7 - - - +
113A LYS* 1.3 62.7 + - + +
114A PHE 3.3 0.3 + - - -
115A LEU* 3.3 28.3 + - + +
117A PHE 5.2 1.5 - - - +
119A VAL* 3.6 40.8 - - + +
----------------------------------------------------------
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