Contacts of the strand formed by residues 122 - 127 (chain F) in PDB entry 3NVQ
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 122 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111F PRO* 3.2 3.6 - - - +
112F TYR* 2.7 74.4 + - + +
113F ARG* 3.3 39.7 + - - +
121F GLY* 1.3 76.9 - - - +
123F LEU* 1.3 60.2 + - - +
136F VAL* 4.4 8.1 - - + -
137F ARG 3.4 17.0 - - - +
138F PRO* 4.0 7.9 - - + -
139F LEU* 3.6 6.7 - - - +
147F LEU* 4.2 20.2 - - + -
148F ARG* 4.7 8.3 - - - +
175F TRP* 6.0 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 123 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58F PHE* 4.4 24.5 - - + -
65F LEU* 4.2 9.9 - - + -
109F LEU* 3.9 16.4 - - + -
110F LEU 3.4 33.9 - - - +
111F PRO* 3.5 11.9 - - + -
112F TYR* 4.4 1.8 - - - -
122F LEU* 1.3 77.6 - - - +
124F LEU* 1.3 64.0 + - - +
125F THR* 3.4 24.6 + - + -
135F GLU 3.4 2.9 - - - +
136F VAL* 3.7 0.7 - - - -
137F ARG* 2.6 51.7 + - + +
138F PRO 4.7 1.8 - - - +
139F LEU* 4.4 12.6 - - + -
142F LEU* 5.0 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 124 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108F LEU* 3.4 3.4 - - + +
109F LEU* 3.2 7.6 + - - -
110F LEU* 2.8 50.3 + - + +
112F TYR* 3.6 23.8 - - + +
123F LEU* 1.3 72.8 - - - +
125F THR* 1.3 60.9 + - - +
134F CYS* 4.3 14.8 - - - -
135F GLU 3.6 3.8 - - - +
136F VAL* 3.9 26.2 - - + -
166F VAL* 3.5 30.3 - - + -
177F LEU* 3.9 32.5 - - + -
210F THR* 4.5 9.0 - - + -
215F LEU* 5.4 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 125 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65F LEU* 4.1 8.1 - - + -
108F LEU 3.2 4.7 - - - -
109F LEU* 4.0 10.8 - - + -
123F LEU* 3.4 30.7 - - + -
124F LEU* 1.3 78.6 - - - +
126F GLY* 1.3 57.5 + - - +
127F TRP* 3.1 28.2 - - - -
134F CYS* 3.3 5.1 - - - -
135F GLU* 3.0 30.2 + - - +
137F ARG* 2.8 35.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 126 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106F SER* 3.5 5.7 - - - -
107F LYS* 2.7 29.5 + - - -
108F LEU* 2.8 28.7 + - - +
125F THR* 1.3 74.4 - - - +
127F TRP* 1.3 62.2 + - - -
133F ALA 3.4 8.1 - - - -
134F CYS* 3.9 10.1 - - - -
154F VAL* 4.4 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 127 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60F ALA* 5.3 0.2 - - - +
62F GLY 4.7 7.0 + - - -
63F SER 4.8 3.4 - - - -
64F CYS 5.1 4.9 + - - -
65F LEU* 4.5 15.0 - - + -
79F LEU* 3.7 25.1 - - + -
81F ARG* 3.6 26.3 - - + +
105F PHE* 3.1 30.7 - - + -
106F SER* 3.7 14.5 - - - +
107F LYS* 4.2 1.8 - - - +
108F LEU 6.0 0.2 - - - -
125F THR* 3.1 48.0 - - + -
126F GLY* 1.3 78.3 - - - -
128F THR* 1.3 61.2 + - - +
129F PHE* 3.2 36.7 - + + +
132F GLY* 3.0 12.0 - - - -
133F ALA 2.8 11.9 + - - +
135F GLU* 3.0 29.8 - - + -
137F ARG* 4.5 0.2 - - - -
154F VAL* 3.0 21.8 - - - +
----------------------------------------------------------
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