Contacts of the strand formed by residues 140 - 145 (chain A) in PDB entry 3NDF
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 SER 140 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A MET* 3.3 16.6 - - - +
116A ASN* 2.7 33.3 + - - -
118A LEU* 3.6 16.1 - - - +
134A VAL* 3.1 27.6 + - - +
135A LYS* 4.0 14.6 + - - +
138A TYR 2.7 4.6 + - - -
139A HIS* 1.3 75.1 - - - +
141A GLU* 1.3 63.0 + - - +
142A ALA 3.9 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A GLY* 5.8 0.9 - - - -
116A ASN 2.7 15.8 + - - +
117A GLY* 3.3 1.6 - - - -
118A LEU 2.6 31.5 + - - -
139A HIS 4.5 5.8 - - - +
140A SER* 1.3 75.2 - - - +
142A ALA* 1.3 57.6 + - - +
143A PHE* 3.2 34.3 - - + -
160A TYR* 3.7 22.3 + - - -
187A TYR* 5.3 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A LEU* 3.5 9.9 - - + -
120A LEU* 4.1 19.7 - - + -
131A LEU* 4.4 21.3 - - + -
140A SER* 3.9 3.0 + - - +
141A GLU* 1.3 71.6 - - - +
143A PHE* 1.3 68.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A GLY* 4.2 4.0 - - - -
118A LEU 2.9 7.8 + - - +
119A PHE* 3.7 39.3 - + + -
120A LEU* 2.8 32.0 + - - +
141A GLU* 3.2 50.7 - - + -
142A ALA* 1.3 78.0 - - - +
144A THR* 1.3 62.8 + - - +
145A VAL* 4.8 3.1 - - + -
156A GLN* 5.1 9.0 - - - +
160A TYR* 3.9 27.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A LEU* 3.3 14.9 + - - +
121A SER 4.4 1.3 - - - +
122A GLU* 3.4 36.1 - - + +
143A PHE* 1.3 75.5 + - - +
145A VAL* 1.3 69.1 + - - +
156A GLN* 4.3 6.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A PHE* 3.8 30.1 - - + -
120A LEU 3.1 5.1 + - - +
121A SER* 3.2 23.2 - - - -
122A GLU* 3.5 9.2 + - - -
143A PHE* 4.8 0.4 - - + -
144A THR* 1.3 79.8 - - - +
146A ASN* 1.3 61.4 + - - +
147A PHE* 3.6 37.3 + - + -
153A ALA* 4.8 13.0 - - + +
156A GLN* 3.2 38.4 - - + +
157A ILE* 6.0 0.9 - - + -
----------------------------------------------------------
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