Contacts of the helix formed by residues 138 - 146 (chain A) in PDB entry 1LF4
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 138 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ALA* 5.6 5.2 - - + +
100A TYR* 3.8 3.4 - - - +
126A LEU* 5.8 1.1 - - - -
127A GLY 3.5 18.8 - - - +
128A TRP* 4.2 1.1 - - + -
129A LYS* 3.6 28.3 - - + +
136A VAL 3.5 1.8 - - - +
137A ASP* 1.3 88.6 - - + +
139A ILE* 1.3 60.2 + - - +
140A VAL 4.5 0.7 - - - +
141A VAL* 3.0 27.8 + - + +
142A GLU* 2.8 26.7 + - - +
315A TYR* 3.5 25.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LEU* 4.6 9.2 - - + -
91A VAL* 5.1 5.2 - - + -
93A VAL* 5.0 10.5 - - + -
98A LEU* 4.1 20.6 - - + -
100A TYR* 3.2 42.6 + - + +
124A LEU* 3.9 38.6 - - + -
125A GLY 4.7 7.0 - - - +
126A LEU* 5.7 3.4 - - + -
138A PRO* 1.3 70.3 - - - +
140A VAL* 1.3 61.5 + - + +
142A GLU* 3.2 4.4 + - - +
143A LEU* 2.8 43.9 + - + +
170A ILE* 6.0 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A LEU* 4.6 12.6 - - + -
138A PRO* 3.3 1.0 - - - +
139A ILE* 1.3 75.6 - - + +
141A VAL* 1.3 66.5 + - - +
143A LEU* 3.4 7.1 + - + -
144A LYS* 3.0 20.4 + - - +
149A ILE* 3.4 16.2 - - + +
152A ALA 3.9 4.9 - - - -
153A LEU* 3.6 37.7 - - - +
154A PHE* 4.0 21.8 - - + -
170A ILE* 3.9 24.2 - - + -
315A TYR* 3.9 14.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A ASP* 4.5 11.9 - - + +
138A PRO* 3.0 32.9 + - + +
140A VAL* 1.3 75.9 - - - +
142A GLU* 1.3 64.2 + - - +
144A LYS* 3.2 8.3 + - - +
145A ASN* 3.1 41.1 + - - +
152A ALA* 4.6 4.9 - - + -
315A TYR* 3.6 39.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A LEU* 3.7 18.2 - - + +
99A PRO 5.5 2.3 - - - +
100A TYR* 4.2 12.9 - - + -
136A VAL* 6.0 0.4 - - + +
137A ASP* 3.7 32.7 - - + +
138A PRO 2.8 15.0 + - - +
139A ILE* 3.4 8.7 - - - +
141A VAL* 1.3 76.5 - - - +
143A LEU* 1.3 63.2 + - - +
145A ASN* 3.1 19.9 + - - +
146A GLN* 3.0 34.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ASP* 5.4 0.4 - - - +
93A VAL* 5.9 3.4 - - + -
96A LEU* 4.2 24.2 - - + -
97A SER 4.5 0.7 - - - +
98A LEU* 4.1 24.7 - - + -
139A ILE* 2.8 33.1 + - + +
140A VAL* 3.7 7.2 - - - +
141A VAL 3.3 0.2 - - - -
142A GLU* 1.3 76.1 - - - +
144A LYS* 1.3 60.7 - - - +
146A GLN* 3.3 7.7 + - - +
148A LYS* 2.9 55.0 + - + +
149A ILE* 3.7 13.5 - - + -
170A ILE* 4.2 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A VAL 3.0 13.4 + - - +
141A VAL 3.4 8.3 - - - +
143A LEU* 1.3 76.6 - - - +
145A ASN* 1.3 62.1 + - - +
147A ASN* 2.9 23.7 + - - +
149A ILE* 3.4 24.4 - - + +
150A GLU 3.4 19.9 + - - -
151A ASN* 3.8 2.0 - - - +
152A ALA* 3.7 28.1 - - + +
316A ASP* 3.0 28.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A ASP* 5.3 3.6 + - - -
141A VAL* 3.1 30.1 + - - +
142A GLU* 3.6 22.6 + - - +
144A LYS* 1.3 80.4 - - - +
146A GLN* 1.3 59.8 + - + +
147A ASN* 3.1 15.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A LEU* 3.5 27.8 - - - +
99A PRO* 4.7 8.7 - - - +
142A GLU* 3.0 23.7 + - - +
143A LEU* 3.7 5.5 - - - +
144A LYS 3.1 0.6 - - - -
145A ASN* 1.3 77.1 - - + +
147A ASN* 1.3 76.5 + - - +
148A LYS* 2.9 49.6 + - + +
----------------------------------------------------------
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