Contacts of the strand formed by residues 129 - 134 (chain A) in PDB entry 1NN5
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 129 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LEU 3.4 1.2 + - - -
9A ILE* 3.5 26.0 - - + -
10A VAL 2.9 24.8 + - - -
127A PRO* 3.3 5.1 + - - +
128A ASP* 1.3 80.3 - - - +
130A VAL* 1.3 66.4 + - - +
131A LEU* 4.0 19.1 - - + -
174A ASN* 3.7 14.4 - - - +
176A LYS* 3.4 37.9 - - + -
194A LEU* 3.8 25.6 - - + +
195A SER* 4.0 11.9 - - - +
198A ALA* 3.9 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A VAL* 3.5 13.5 - - + +
12A GLU* 4.3 2.5 - - + -
100A PHE* 3.9 30.3 - - + -
127A PRO* 3.7 21.8 - - + +
129A LEU* 1.3 76.1 - - - +
131A LEU* 1.3 65.3 + - - +
132A PHE 3.7 0.5 + - - -
173A LEU* 4.4 15.5 - - + -
174A ASN 2.9 16.0 + - - +
175A TRP* 3.4 39.6 - - + -
176A LYS 2.9 25.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ILE* 3.9 26.0 - - + -
10A VAL 2.8 10.2 + - - +
11A LEU* 3.6 13.6 - - + -
12A GLU* 2.8 30.7 + - - +
129A LEU* 4.0 17.9 - - + -
130A VAL* 1.3 74.1 - - - +
132A PHE* 1.3 60.5 + - - +
133A LEU* 3.9 15.0 - - + +
176A LYS* 3.4 11.0 - - + -
178A VAL* 3.8 12.1 - - + -
191A ILE* 3.8 27.4 - - + -
194A LEU* 3.7 32.5 - - + -
195A SER* 4.2 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A GLU* 3.5 9.4 - - + -
13A GLY* 3.6 27.8 - - - -
14A VAL* 4.4 4.0 - - + -
130A VAL 3.7 0.6 + - - -
131A LEU* 1.3 72.3 - - - +
133A LEU* 1.3 66.3 + - - +
134A GLN* 3.3 28.6 + - + +
161A LEU* 3.9 26.9 - - + -
164A PHE* 3.5 29.6 - + + -
165A HIS* 4.8 2.7 - + - -
168A MET* 3.4 29.2 - - + -
175A TRP* 4.2 12.8 - + + -
176A LYS 2.9 8.7 + - - -
177A MET* 3.7 22.4 - - + -
178A VAL 2.9 26.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 4.2 8.7 - - + -
12A GLU 2.9 22.1 + - - +
13A GLY* 3.8 8.3 - - - -
14A VAL* 4.4 2.6 + - - +
17A ALA* 3.5 28.0 - - + +
18A GLY 3.7 32.5 - - - +
19A LYS* 3.8 8.5 - - + +
22A GLN* 4.0 16.8 - - + -
131A LEU* 4.1 21.3 - - + +
132A PHE* 1.3 75.6 - - - +
134A GLN* 1.3 63.5 + - - +
135A LEU 3.8 0.9 + - - -
178A VAL* 3.7 13.7 - - + -
180A ALA* 3.8 15.5 - - + -
187A VAL* 4.8 0.9 - - + -
191A ILE* 4.2 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A PHE* 3.7 30.3 - - + +
133A LEU* 1.3 71.8 - - - +
135A LEU* 1.3 62.6 + - - +
165A HIS* 4.4 15.9 + - - -
177A MET* 3.5 32.1 - - - +
178A VAL 2.8 17.8 + - - +
179A ASP* 3.9 6.1 - - - +
180A ALA* 2.9 28.2 + - - +
181A SER* 3.9 2.3 + - - -
----------------------------------------------------------
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