Contacts of the helix formed by residues 141 - 154 (chain A) in PDB entry 5LDH
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 PRO 141 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A ARG* 4.1 7.1 - - + +
110A LEU* 3.3 26.5 - - + +
111A ASN* 4.6 3.6 - - - +
112A LEU 4.3 6.3 - - - +
139A SER 3.2 5.8 - - - +
140A ASN* 1.3 92.7 - - + -
142A VAL* 1.3 68.5 + - + +
143A ASP* 3.2 6.4 + - + +
144A ILE* 3.3 39.4 - - + +
145A LEU* 3.5 5.2 - - + +
194A GLU* 6.4 1.8 - - + -
195A HIS* 5.7 3.1 - - + -
322A LEU* 5.6 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A VAL* 3.6 13.3 - - - +
138A VAL* 4.6 9.6 - - + -
139A SER 4.4 3.4 - - - +
140A ASN 2.5 17.3 + - - +
141A PRO* 1.3 69.8 - - + +
143A ASP* 1.3 82.9 + - - +
145A LEU* 3.2 4.2 + - - +
146A THR* 2.9 21.3 + - - +
162A GLY* 3.4 37.0 - - - +
163A SER* 3.8 9.4 - - - +
164A GLY* 4.0 16.6 - - - +
194A GLU 4.7 9.9 - - - +
195A HIS* 4.9 6.5 - - + +
272A SER* 4.0 9.6 - - - +
332A LNC 5.2 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A PRO* 3.2 3.5 - - + +
142A VAL* 1.3 84.9 + - - +
144A ILE* 1.3 66.2 + - - +
146A THR* 2.3 36.7 - - - +
147A TYR* 3.4 1.9 + - - +
193A GLY 4.0 7.6 - - - +
194A GLU* 4.1 12.6 - - - +
272A SER* 3.9 11.1 + - - -
286A PHE* 4.2 17.0 - - + +
287A LEU* 2.0 58.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A ASN 4.9 0.9 - - - +
112A LEU 4.6 0.2 - - - +
113A VAL* 3.1 37.2 - - + -
141A PRO* 3.3 30.2 + - + +
143A ASP* 1.3 78.6 - - - +
145A LEU* 1.3 102.7 - - + +
147A TYR* 3.4 10.7 - - + -
148A VAL* 2.0 31.1 + - + +
286A PHE* 5.2 6.6 - - - -
322A LEU* 4.8 14.8 - - + -
326A GLN* 2.9 40.8 - - + +
330A LYS* 6.0 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A LEU 5.1 0.9 - - - +
113A VAL* 4.6 11.2 - - + -
116A ASN* 3.7 21.3 - - + +
120A PHE* 4.1 12.3 - - + -
137A VAL* 3.3 20.2 - - + -
139A SER* 3.1 44.6 - - - +
141A PRO* 3.5 6.3 - - + +
142A VAL* 3.2 3.4 + - - +
143A ASP 2.7 4.2 + - - -
144A ILE* 1.3 104.6 - - + +
146A THR* 1.3 52.9 + - - +
148A VAL* 2.2 37.9 + - + -
149A ALA* 2.3 39.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A VAL* 4.1 6.4 - - - +
142A VAL 2.9 14.1 + - - +
143A ASP* 2.3 50.1 + - - +
145A LEU* 1.3 71.6 - - - +
147A TYR* 1.3 59.4 + - + +
149A ALA* 4.5 3.6 - - - -
150A TRP* 2.6 32.4 + - - +
160A VAL* 2.0 49.8 + - - +
161A ILE 4.9 0.2 - - - -
162A GLY* 4.3 13.9 - - - -
272A SER* 4.0 14.7 + - - +
273A THR* 5.1 6.5 + - - +
286A PHE* 5.2 4.7 - - + -
287A LEU 5.8 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A ASP 3.4 3.9 + - - +
144A ILE* 3.4 14.1 - - + +
145A LEU 3.2 0.4 - - - -
146A THR* 1.3 80.7 - - + +
148A VAL* 1.3 74.1 + - + +
150A TRP* 2.7 49.4 - + + -
151A LYS* 2.9 31.7 + - + +
160A VAL* 4.9 0.2 - - - -
284A GLU* 4.3 32.8 - - + -
286A PHE* 4.5 23.6 - + + -
323A TRP* 6.5 0.9 - + - -
326A GLN* 4.4 15.0 + - - -
330A LYS* 3.2 40.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A VAL* 6.0 0.7 - - + -
117A VAL* 5.8 10.1 - - + -
120A PHE* 5.8 9.0 - - + -
144A ILE* 2.0 39.3 - - + +
145A LEU* 2.2 49.1 + - + +
147A TYR* 1.3 91.4 - - + +
149A ALA* 1.3 71.8 + - - +
151A LYS* 3.6 1.1 - - - +
152A LEU* 3.1 40.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A PHE* 5.8 2.9 - - + -
124A ILE* 5.8 8.1 - - + -
135A ILE* 4.5 16.6 - - + -
137A VAL* 3.6 28.5 - - + -
145A LEU* 2.3 29.6 + - + +
146A THR* 3.7 2.9 - - - +
148A VAL* 1.3 69.9 - - + +
150A TRP* 1.3 55.7 + - - +
152A LEU* 5.4 1.3 - - - -
153A SER* 2.4 48.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A THR 2.6 15.9 + - - +
147A TYR* 2.7 63.9 - + + -
149A ALA* 1.3 71.7 - - - +
151A LYS* 1.3 84.0 + - + +
153A SER* 3.9 3.6 - - - -
154A GLY* 2.6 33.9 + - - +
155A LEU* 2.9 10.3 + - - +
156A PRO* 2.5 58.9 - - + +
159A ARG* 5.8 0.4 - - - -
160A VAL* 2.1 36.5 - - + +
284A GLU* 4.3 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A TYR* 2.9 39.2 + - + +
148A VAL* 3.6 3.6 - - - +
149A ALA 3.2 0.2 - - - -
150A TRP* 1.3 111.5 - - + +
152A LEU* 1.3 77.0 + - + +
154A GLY* 4.2 3.3 + - - -
284A GLU* 3.9 14.1 + - - -
330A LYS* 5.2 12.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A VAL* 5.9 4.5 - - + -
121A LYS* 4.6 13.0 - - + -
124A ILE* 6.2 5.6 - - + -
148A VAL* 3.1 30.4 + - + +
149A ALA* 5.4 1.3 - - - -
151A LYS* 1.3 90.7 - - + +
153A SER* 1.3 64.5 + - - +
330A LYS* 5.8 3.4 - - - +
331A LEU* 3.6 45.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ILE* 6.2 4.5 - - - -
128A VAL* 3.9 33.8 - - - +
135A ILE* 5.6 9.4 - - - +
149A ALA* 2.4 40.1 + - - -
150A TRP* 3.3 4.5 - - - -
151A LYS 3.1 0.4 - - - -
152A LEU* 1.3 78.0 - - - +
154A GLY* 1.3 58.9 + - - -
159A ARG* 4.4 14.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A TRP* 2.6 15.5 + - - +
151A LYS 4.2 2.8 + - - -
152A LEU 3.9 0.4 - - - -
153A SER* 1.3 78.6 - - - +
155A LEU* 1.3 85.9 - - - +
159A ARG* 3.0 24.0 + - - -
----------------------------------------------------------
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