Contacts of the strand formed by residues 139 - 144 (chain B) in PDB entry 3NDM
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 139 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B ARG* 3.9 17.7 - - + +
128B MET* 2.7 20.5 + - + +
129B ALA* 3.7 39.7 - - + +
138B GLN* 1.3 77.3 - - - +
140B PHE* 1.3 67.3 + - - +
141B TYR 3.3 22.4 - - - +
142B ALA* 4.1 13.7 - - + -
151B MET* 3.5 45.1 - - + -
152B VAL 3.3 11.4 - - - +
153B MET* 3.7 6.1 - - + -
399B TYR* 4.3 8.1 - - + -
401B SER 4.3 3.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 140 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B TYR* 3.3 34.1 - + + +
138B GLN* 3.5 42.2 - - + -
139B LEU* 1.3 77.9 - - - +
141B TYR* 1.3 89.2 + - + +
152B VAL 2.9 8.2 + - - +
153B MET 4.1 1.6 - - - -
154B GLU* 3.5 34.5 - - + -
399B TYR* 3.8 5.5 - - - +
401B SER 2.5 34.2 + - - +
402B ASN 5.3 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 141 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A PHE* 4.0 19.3 - + - -
11A PHE* 6.1 1.1 - + - -
71B MET* 3.3 38.4 - - + -
76B TYR* 3.1 26.5 - - - -
95B HIS* 4.8 4.1 - + - -
98B THR* 5.7 0.3 + - - -
102B TYR* 3.9 26.2 + + - -
139B LEU* 3.3 10.9 - - - +
140B PHE* 1.3 101.3 - - + +
142B ALA* 1.3 61.1 + - - +
143B PHE* 4.4 0.2 - - + -
152B VAL* 2.9 40.5 + - + -
399B TYR 3.2 7.6 - - - +
400B TYR* 4.2 15.0 - + + -
401B SER* 4.2 14.1 - - - -
402B ASN 5.3 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 142 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B ARG* 4.5 0.7 - - - -
139B LEU* 4.1 16.8 - - + -
141B TYR* 1.3 75.9 - - - +
143B PHE* 1.3 70.0 + - - +
150B TYR 3.3 11.0 - - - +
151B MET* 4.7 1.1 - - + -
397B PHE* 3.9 26.9 - - + +
398B THR* 3.2 5.2 - - - +
399B TYR* 2.8 42.0 + - + +
400B TYR* 5.0 1.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 143 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B MET* 3.5 59.7 - - + +
72B LYS* 5.3 0.2 - - - -
73B ALA* 4.3 15.7 - - - -
76B TYR* 4.6 4.7 - + - -
104B MET* 4.0 14.6 - - - -
141B TYR* 4.4 0.2 - - + -
142B ALA* 1.3 84.6 - - - +
144B GLN* 1.3 67.5 + - - +
149B LEU* 3.4 3.5 - - - -
150B TYR* 2.8 72.9 + + + -
152B VAL* 3.7 15.7 - - + -
397B PHE* 3.9 6.9 - - - -
398B THR* 3.8 20.2 - - + +
400B TYR* 5.2 2.9 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 144 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B ASP* 3.4 31.7 + - - +
35B ASP* 4.5 15.0 - - - +
36B ALA* 5.4 1.9 - - - +
109B LYS* 2.4 31.8 + - - +
143B PHE* 1.3 82.2 - - - +
145B ASP* 1.3 61.4 + - - +
148B TYR 3.2 5.4 - - - -
149B LEU* 3.5 14.1 - - + -
150B TYR* 4.2 4.9 - - - -
391B GLN* 3.3 9.9 - - - +
394B PHE* 2.3 34.2 + - - +
395B VAL* 4.3 0.7 - - - +
397B PHE* 4.1 5.9 - - - +
398B THR* 4.2 7.4 + - - +
----------------------------------------------------------
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