Contacts of the helix formed by residues 127 - 144 (chain F) in PDB entry 1TYE
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 ASP 127 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123F SER 3.0 6.9 - - - +
124F MET* 2.8 23.6 + - + +
126F ASP* 1.3 86.1 - - - +
128F LEU* 1.3 65.9 + - - +
129F TRP 3.2 2.9 - - - -
130F SER* 3.0 25.3 + - - +
131F ILE* 3.1 16.7 + - + +
251F ASP* 3.0 16.0 - - - +
311F THR* 4.4 13.7 - - + +
333F LEU* 5.7 1.3 - - + -
1416F CA 2.3 30.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 128 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118F MET* 4.7 1.8 - - + -
119F ASP 5.6 0.2 - - - +
120F LEU* 4.6 11.0 - - + -
124F MET* 2.6 12.4 + - + +
125F LYS* 3.2 16.7 + - + +
127F ASP* 1.3 73.7 - - - +
129F TRP* 1.3 57.9 + - - +
131F ILE* 3.2 24.2 - - + +
132F GLN* 3.0 52.9 + - + +
210F GLN 3.4 26.7 - - - +
211F SER* 3.8 14.6 - - - -
212F VAL* 4.3 15.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 129 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125F LYS 4.8 0.6 + - - -
126F ASP 5.2 2.2 - - - +
127F ASP 3.2 1.0 - - - -
128F LEU* 1.3 77.8 - - - +
130F SER* 1.3 59.2 + - - +
132F GLN* 3.1 18.2 + - + +
133F ASN* 2.7 67.7 + - + +
208F LYS* 5.6 6.7 - - - +
335F MET* 3.6 50.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 130 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126F ASP 5.1 1.9 + - - -
127F ASP* 3.0 19.4 + - - -
129F TRP* 1.3 87.8 - - - +
131F ILE* 1.3 56.7 + - - +
133F ASN* 3.7 3.4 + - - +
134F LEU* 3.0 27.5 + - - +
333F LEU* 4.0 13.1 - - - +
334F SER* 3.7 21.7 - - - +
335F MET* 3.7 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 131 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116F TYR* 2.9 34.9 + - + +
118F MET* 3.5 31.6 - - + -
119F ASP 4.0 10.3 - - - +
120F LEU* 4.2 0.9 - - + -
124F MET* 3.6 31.2 - - + -
127F ASP* 3.1 9.1 + - + +
128F LEU* 3.2 30.3 - - + +
130F SER* 1.3 73.2 - - - +
132F GLN* 1.3 60.5 - - - +
133F ASN 3.3 0.2 - - - -
134F LEU* 4.3 0.9 - - - -
135F GLY* 3.0 14.2 + - - -
249F THR* 4.2 7.9 - - - +
333F LEU* 3.6 30.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 132 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118F MET* 4.5 2.2 - - + -
128F LEU* 3.0 42.1 + - + +
129F TRP* 3.4 19.7 - - + +
131F ILE* 1.3 78.9 - - - +
133F ASN* 1.3 60.7 + - - +
135F GLY* 3.4 1.4 + - - -
136F THR* 3.3 25.6 + - - -
207F VAL* 3.6 30.4 + - + +
208F LYS* 3.5 38.1 + - + +
210F GLN 3.2 25.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 133 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129F TRP* 2.7 47.5 + - + +
130F SER 3.7 5.0 + - - +
132F GLN* 1.3 72.4 - - - +
134F LEU* 1.3 54.1 + - - +
135F GLY 3.0 5.0 + - - -
136F THR* 3.1 5.0 + - - -
137F LYS* 2.7 56.3 + - - +
208F LYS* 5.5 3.6 - - - +
334F SER 5.2 0.8 + - - -
335F MET 3.4 21.2 + - - -
337F SER* 3.3 23.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 134 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116F TYR* 3.4 25.1 - - + +
130F SER 3.0 16.4 + - - +
132F GLN 3.5 0.2 - - - -
133F ASN* 1.3 78.8 - - - +
135F GLY* 1.3 57.0 + - - +
137F LYS* 4.4 5.4 - - - -
138F LEU* 2.9 32.6 + - + +
247F VAL* 4.8 1.1 - - + -
249F THR* 4.1 1.8 - - + -
309F ALA* 4.0 12.1 - - + -
333F LEU* 3.7 23.1 - - + -
334F SER 5.4 1.6 - - - +
337F SER* 4.4 11.4 - - - +
340F VAL* 3.7 42.2 - - + -
341F LEU* 3.8 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 135 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116F TYR* 3.7 21.1 - - - -
131F ILE 3.0 15.9 + - - -
132F GLN 3.4 2.4 + - - -
133F ASN 3.0 1.6 - - - -
134F LEU* 1.3 77.3 - - - +
136F THR* 1.3 63.7 + - - +
138F LEU* 3.4 15.5 + - - +
139F ALA 3.8 2.1 + - - -
203F PHE* 3.0 26.4 - - - -
207F VAL* 4.7 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 136 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132F GLN 3.3 14.7 + - - -
133F ASN* 3.1 4.3 + - - -
135F GLY* 1.3 71.4 - - - +
137F LYS* 1.3 61.3 + - + +
138F LEU 3.0 8.7 + - - -
139F ALA* 3.3 13.9 + - - +
140F THR* 3.5 13.7 + - - +
200F VAL* 5.7 0.2 - - - +
204F ASN* 3.3 46.9 + - + +
207F VAL* 4.8 3.1 - - - +
208F LYS* 4.1 20.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 137 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133F ASN* 2.7 36.8 + - - +
134F LEU* 4.1 1.8 - - - -
136F THR* 1.3 73.4 - - + +
138F LEU* 1.3 59.0 + - - +
140F THR* 3.9 16.7 + - + +
141F GLN 3.6 12.8 + - - -
335F MET 5.6 0.4 + - - -
337F SER* 3.6 36.1 + - - +
341F LEU* 3.8 17.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 138 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114F ILE* 4.2 22.0 - - + -
116F TYR* 4.1 22.2 - - + -
134F LEU* 2.9 26.3 + - + +
135F GLY 3.4 9.0 - - - +
136F THR 3.0 0.2 - - - -
137F LYS* 1.3 75.3 - - - +
139F ALA* 1.3 64.7 + - - +
140F THR 3.1 1.8 - - - -
141F GLN* 3.3 13.6 + - + +
142F MET* 3.4 16.2 + - - +
151F ILE* 5.2 5.6 - - + -
203F PHE* 5.9 0.2 - - + -
247F VAL* 4.0 24.5 - - + -
340F VAL* 5.1 4.0 - - + -
341F LEU* 3.7 23.6 - - + -
344F ILE* 4.0 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 139 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114F ILE* 6.3 0.2 - - - -
135F GLY 3.8 4.3 + - - +
136F THR 3.3 8.4 + - - +
138F LEU* 1.3 78.9 - - - +
140F THR* 1.3 56.9 + - - +
141F GLN 3.4 0.2 - - - -
142F MET* 3.6 1.4 + - - +
143F ARG* 3.1 30.5 + - - +
149F LEU* 4.3 10.5 - - + +
151F ILE* 4.1 23.7 - - + +
200F VAL* 3.6 35.4 - - + +
203F PHE* 4.9 4.9 - - + -
204F ASN* 5.0 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 140 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136F THR* 3.5 12.4 + - - +
137F LYS* 3.9 21.4 - - + +
138F LEU 3.1 0.4 - - - -
139F ALA* 1.3 78.7 - - - +
141F GLN* 1.3 63.6 + - - +
143F ARG* 3.4 4.3 + - - +
144F LYS* 3.3 56.6 + - + +
200F VAL* 6.2 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 141 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137F LYS 3.6 3.9 + - - +
138F LEU* 3.3 10.2 + - + +
140F THR* 1.3 82.9 - - - +
142F MET* 1.3 60.4 + - + +
144F LYS* 3.8 11.7 + - - +
145F LEU* 3.6 20.0 + - + +
341F LEU* 3.9 41.5 - - + +
344F ILE* 4.7 9.2 - - + -
345F VAL* 3.3 33.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 142 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112F VAL* 3.4 44.2 - - + -
114F ILE* 3.5 25.1 - - + -
138F LEU 3.4 10.0 + - - +
139F ALA* 4.9 0.2 - - - -
140F THR 3.3 0.2 - - - -
141F GLN* 1.3 74.4 - - - +
143F ARG* 1.3 61.5 + - - +
144F LYS 3.2 1.3 - - - -
145F LEU* 3.2 15.3 + - - -
146F THR* 3.0 49.3 + - + +
149F LEU* 3.6 22.4 - - + -
245F LEU* 5.2 2.2 - - + -
344F ILE* 3.1 32.3 - - + +
348F TYR* 4.2 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 143 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139F ALA 3.1 18.9 + - - +
140F THR* 3.4 6.9 + - - +
142F MET* 1.3 76.5 - - - +
144F LYS* 1.3 61.3 + - + +
145F LEU 3.1 4.0 + - - -
146F THR 3.5 18.5 + - - +
147F SER* 3.5 39.7 + - - +
149F LEU* 4.3 15.0 - - - +
198F ASP 5.5 1.8 + - - -
200F VAL* 4.6 19.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 144 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140F THR* 3.3 40.0 + - + +
141F GLN* 3.8 9.7 + - - +
142F MET 3.2 0.6 - - - -
143F ARG* 1.3 78.1 - - + +
145F LEU* 1.3 62.0 + - - +
----------------------------------------------------------
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