Contacts of the helix formed by residues 141 - 155 (chain A) in PDB entry 1YL5
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 SER 141 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A GLU* 3.1 13.9 + - - +
132A HIS* 3.7 17.3 - - - -
136A LYS* 3.5 30.7 - - - +
138A ASP* 3.9 3.2 + - - -
140A PRO* 1.3 78.2 - - - +
142A GLY* 1.3 65.1 + - - +
143A THR* 3.8 7.3 + - - -
144A ALA* 3.2 22.7 + - - +
145A ALA* 3.0 21.1 + - - +
194A GLN* 4.4 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A LYS* 5.1 0.8 - - - +
138A ASP* 3.8 10.7 + - - -
141A SER* 1.3 72.8 - - - +
143A THR* 1.3 50.9 + - - +
145A ALA* 3.2 8.0 + - - +
146A ARG* 2.6 45.2 + - - +
149A LYS* 5.7 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A ASN* 3.4 15.6 + - - +
109A ALA* 5.1 6.3 - - + -
113A MET* 4.0 17.5 - - + -
132A HIS* 6.4 0.4 - - - -
141A SER* 3.3 6.0 - - - -
142A GLY* 1.3 76.2 - - - +
144A ALA* 1.3 52.6 + - - +
146A ARG* 2.9 26.2 + - - +
147A THR* 2.5 44.9 + - - +
194A GLN* 3.4 19.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A VAL* 4.1 7.3 - - + +
130A GLU* 3.9 14.6 - - + -
140A PRO* 4.0 2.9 - - + -
141A SER* 3.2 21.3 + - - +
143A THR* 1.3 71.9 - - - +
145A ALA* 1.3 61.8 + - - +
147A THR* 3.2 2.7 + - - -
148A ALA* 2.8 30.5 + - - +
182A VAL* 3.8 25.0 - - + +
194A GLN* 3.1 20.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A PRO* 4.7 12.2 - - + +
141A SER 3.0 13.5 + - - +
142A GLY* 3.5 10.1 - - - +
144A ALA* 1.3 75.3 - - - +
146A ARG* 1.3 62.5 + - - +
148A ALA* 3.4 5.3 + - - +
149A LYS* 3.1 48.9 + - - +
177A VAL* 4.6 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A PRO* 4.0 36.3 + - - +
104A ASN* 3.1 24.5 - - - +
113A MET* 3.5 26.5 - - - +
142A GLY* 2.6 31.0 + - - +
143A THR* 2.9 29.5 + - - +
145A ALA* 1.3 74.0 - - - +
147A THR* 1.3 63.3 + - - +
149A LYS* 3.8 12.1 - - - +
150A LEU* 3.0 35.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A SER 6.0 0.2 - - - -
113A MET* 3.4 19.9 - - + +
116A ALA* 4.1 12.1 - - + -
128A VAL* 4.4 3.1 - - + -
143A THR 2.5 28.1 + - - -
144A ALA* 3.5 4.7 - - - -
146A ARG* 1.3 71.7 - - - +
148A ALA* 1.3 60.2 + - - +
150A LEU* 3.1 11.8 + - + +
151A ILE* 2.8 42.5 + - + +
194A GLN* 3.1 27.2 + - - +
196A VAL* 3.8 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A VAL* 4.4 4.4 - - + +
144A ALA 2.8 20.3 + - - +
145A ALA 3.9 1.1 - - - +
147A THR* 1.3 72.5 - - - +
149A LYS* 1.3 52.5 + - - +
151A ILE* 3.0 9.5 + - - +
152A ALA* 2.8 32.4 + - - +
177A VAL* 3.7 17.7 - - + -
180A ILE* 3.5 22.4 - - + +
182A VAL* 3.6 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A ALA* 3.1 34.8 + - - +
146A ARG* 3.8 9.1 - - - +
148A ALA* 1.3 72.9 - - - +
150A LEU* 1.3 63.3 + - - +
152A ALA* 3.4 5.2 + - - +
153A GLU* 3.1 24.3 + - - +
177A VAL* 3.7 14.6 - - + -
178A ASP* 3.7 25.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A MET* 3.9 38.4 - - + +
116A ALA* 6.1 0.4 - - + -
117A LYS* 3.8 35.5 - - + +
146A ARG* 3.0 32.8 + - + +
147A THR* 3.1 17.5 + - + +
149A LYS* 1.3 74.6 - - - +
151A ILE* 1.3 59.7 + - + +
153A GLU* 3.4 6.8 + - - +
154A ALA* 3.0 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ALA* 4.2 20.6 - - + +
117A LYS* 5.7 0.4 - - - +
120A ALA* 4.0 11.2 - - + -
126A ALA* 3.7 20.0 - - + -
128A VAL* 4.0 17.9 - - + -
147A THR* 2.8 23.0 + - + +
148A ALA* 3.0 7.4 + - - +
150A LEU* 1.3 73.4 - - + +
152A ALA* 1.3 67.0 + - - +
154A ALA* 3.1 2.5 + - - +
155A ARG* 3.0 49.4 + - - +
180A ILE* 3.8 10.1 - - + -
196A VAL* 3.4 33.0 - - + -
198A PHE* 4.2 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A ALA 2.8 14.5 + - - +
149A LYS 3.5 9.2 - - - +
151A ILE* 1.3 74.1 - - - +
153A GLU* 1.3 61.2 + - - +
155A ARG* 3.3 6.5 + - - +
156A LYS* 3.2 19.6 + - - +
178A ASP* 3.3 45.1 - - + +
180A ILE* 3.9 9.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A LYS 3.1 17.5 + - - +
150A LEU* 3.7 7.0 - - - +
152A ALA* 1.3 73.2 - - - +
154A ALA* 1.3 66.3 + - - +
155A ARG 3.2 0.9 + - - -
156A LYS* 3.2 49.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A LYS* 3.7 23.3 - - + +
120A ALA* 3.7 19.1 - - + -
121A ARG* 3.7 19.8 - - + +
150A LEU 3.0 17.5 + - - +
151A ILE* 3.1 5.4 + - - +
153A GLU* 1.3 77.9 - - - +
155A ARG* 1.3 58.3 + - - +
156A LYS* 3.4 2.9 + - - +
158A LEU* 5.2 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A ALA* 3.5 32.3 + - + +
121A ARG 4.2 0.4 - - - +
123A PHE 3.1 7.7 + - - -
124A ASP* 2.4 39.2 + - - +
125A SER 4.5 0.4 - - - -
126A ALA* 4.1 9.1 - - - +
151A ILE* 3.0 35.5 + - - +
152A ALA* 3.3 7.2 + - - +
153A GLU 3.1 0.4 - - - -
154A ALA* 1.3 77.2 - - - +
156A LYS* 1.3 63.8 + - - +
157A GLY 3.4 0.3 + - - -
158A LEU* 3.0 37.5 + - + +
159A PRO 4.2 13.8 + - - +
160A PRO* 5.4 0.8 - - - +
161A ASN* 2.6 27.4 + - - +
180A ILE* 3.7 16.2 - - - +
----------------------------------------------------------
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