Contacts of the strand formed by residues 137 - 141 (chain A) in PDB entry 2N8A
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 VAL 137 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A ALA* 5.7 0.7 - - + -
116A GLU 3.8 9.6 - - - +
117A TYR* 3.1 23.1 - - + -
132A ILE* 5.1 1.4 - - - +
135A GLY 4.7 0.4 - - - +
136A GLN* 1.3 76.5 - - - +
138A ARG* 1.3 66.2 + - - +
139A LEU* 5.6 1.3 - - + -
159A HIS* 4.8 2.8 - - - -
160A PRO* 3.3 31.0 - - + +
187A LEU* 5.1 6.7 - - + -
191A ASP* 2.9 30.3 - - - +
195A LEU* 4.6 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A ALA 4.1 0.2 - - - +
115A ALA* 3.5 3.6 - - - +
116A GLU* 2.7 66.9 + - - +
118A ALA* 3.2 22.0 - - - +
119A LYS 3.1 20.0 - - - +
123A SER* 4.1 12.6 + - - -
132A ILE* 4.3 17.2 - - + +
136A GLN 3.9 2.2 - - - +
137A VAL* 1.3 78.3 - - - +
139A LEU* 1.3 64.4 + - - +
157A TRP* 2.9 56.5 - - + +
158A TYR 3.5 12.3 - - - +
159A HIS* 5.4 0.4 - - - -
160A PRO* 4.5 1.1 - - - -
44B C 2.7 37.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A ALA 3.3 7.9 - - - +
115A ALA* 3.2 32.5 - - + -
137A VAL* 5.6 1.3 - - + -
138A ARG* 1.3 75.9 - - - +
140A SER* 1.3 64.6 + - - +
157A TRP* 3.3 2.7 - - - -
158A TYR* 2.8 32.4 + - - +
160A PRO* 3.7 25.7 - - + -
163A PHE* 3.7 35.4 - - + -
181A LEU* 3.7 19.5 - - + -
195A LEU* 3.9 15.3 - - + -
198A GLN* 3.9 15.7 - - - +
199A LEU* 4.5 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ASP 3.6 0.5 - - - +
113A PHE* 3.3 8.1 - - - +
114A ALA* 3.0 41.8 + - - +
139A LEU* 1.3 76.3 - - - +
141A LYS* 1.3 60.3 + - - +
142A LYS* 3.8 0.9 + - - +
155A ASP* 3.9 11.3 + - - -
156A ARG 3.0 14.6 - - - -
157A TRP* 2.7 42.4 - - - -
158A TYR* 4.5 0.2 - - - -
163A PHE* 4.0 9.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ASP* 3.4 10.6 + - - +
113A PHE* 3.2 22.2 - - + -
140A SER* 1.3 72.0 - - - +
142A LYS* 1.3 99.5 + - - +
143A MET* 3.3 24.7 + - - +
156A ARG* 3.1 28.3 + - + +
158A TYR* 4.7 0.4 - - + -
163A PHE* 4.1 5.7 - - + -
169A GLU 5.5 0.2 - - - +
170A LEU* 3.1 59.0 + - + +
171A GLY* 5.9 0.2 - - - -
----------------------------------------------------------
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