Contacts of the strand formed by residues 125 - 131 (chain F) in PDB entry 2Q5E
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 PHE 125 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113F VAL* 5.2 0.2 - - + -
123F ALA* 3.9 3.9 - - - +
124F ASP* 1.3 92.3 - - + +
126F ILE* 1.3 67.2 + - - +
127F VAL* 4.2 1.3 - - + -
138F VAL 3.7 0.2 - - - +
139F TYR* 3.7 0.3 - - - -
140F VAL* 2.8 66.7 + - + +
142F LYS* 3.6 35.0 - - + -
173F VAL* 4.6 6.5 - - + -
176F LEU* 3.8 62.1 - - + -
177F LEU* 4.0 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 126 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123F ALA* 4.8 7.2 - - + +
125F PHE* 1.3 80.0 - - - +
127F VAL* 1.3 70.2 + - - +
128F PRO* 4.0 6.5 - - + +
137F GLN* 3.3 45.5 - - + +
138F VAL 3.2 4.0 - - - +
139F TYR* 3.8 32.3 - - + -
176F LEU* 4.8 2.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 127 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125F PHE* 5.1 1.1 - - + -
126F ILE* 1.3 79.9 - - - +
128F PRO* 1.3 71.3 - - + +
129F ILE* 3.2 20.3 - - + +
138F VAL* 2.9 46.5 + - + +
140F VAL* 4.0 17.7 - - + -
172F PRO* 4.0 25.4 - - + +
173F VAL* 4.0 12.1 - - + -
176F LEU* 3.8 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 128 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126F ILE* 4.0 7.6 - - + +
127F VAL* 1.3 88.0 - - + +
129F ILE* 1.3 64.7 + - - +
135F THR* 4.8 11.9 - - - +
136F HIS 3.3 9.6 - - - +
137F GLN* 3.7 19.5 - - - +
172F PRO* 5.3 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 129 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117F PHE* 5.2 6.5 - - + -
127F VAL* 3.2 34.7 + - + +
128F PRO* 1.3 77.5 - - - +
130F GLU* 1.3 73.9 + - - +
131F ILE* 3.8 12.3 + - + +
135F THR* 4.3 2.2 - - - -
136F HIS* 2.8 34.4 + - - +
138F VAL* 3.5 23.6 - - + -
168F LYS* 4.0 41.3 - - + +
169F TYR* 4.6 19.5 - - + -
172F PRO* 4.7 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 130 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C GLU* 5.3 14.8 - - + +
168C LYS* 5.0 14.1 - - - +
128F PRO 4.3 0.2 - - - -
129F ILE* 1.3 82.7 - - - +
131F ILE* 1.3 62.6 + - - +
132F GLU* 3.4 8.7 + - - -
133F GLY* 2.7 48.4 + - - +
134F THR 3.3 7.9 - - - +
135F THR* 3.9 15.3 - - + +
168F LYS* 4.1 12.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 131 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194D PHE* 4.4 28.5 - - + -
199D TYR* 5.7 2.7 - - - +
117F PHE* 4.5 11.2 - - + -
129F ILE* 3.9 15.5 - - + +
130F GLU* 1.3 80.5 - - - +
132F GLU* 1.3 80.9 + - + +
133F GLY 2.5 16.6 + - - -
134F THR* 2.7 29.4 + - - +
136F HIS* 3.5 26.5 - - + +
168F LYS* 4.0 24.0 - - - +
----------------------------------------------------------
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