Contacts of the helix formed by residues 119 - 135 (chain Y) in PDB entry 1T6B
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 TYR 119 (chain Y).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338X LEU* 3.6 7.4 - - - +
341X ALA* 2.4 38.2 + - + -
342X GLY* 4.7 4.5 - - - -
343X GLU 5.4 0.2 + - - -
659X ARG* 3.5 32.7 + - - -
662X MET* 2.9 23.8 - - + +
85Y PHE* 3.6 9.6 - - + +
86Y SER 2.8 20.7 + - - +
87Y SER* 3.8 14.6 - - - +
88Y GLN 5.8 0.2 - - - +
117Y GLU* 3.8 20.4 - - + -
118Y THR* 1.3 77.5 - - - +
120Y ILE* 1.3 65.4 + - - +
121Y HIS* 3.1 28.3 - + + -
122Y GLU* 2.9 30.3 + - + +
123Y GLY 3.6 2.4 + - - -
155Y VAL* 4.3 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 120 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48Y VAL* 4.9 2.5 - - + -
85Y PHE* 3.5 32.9 - - + -
118Y THR 3.2 3.8 + - - -
119Y TYR* 1.3 74.6 - - - +
121Y HIS* 1.3 65.6 + - - +
123Y GLY* 3.0 12.5 + - - -
124Y LEU* 3.0 25.9 + - + +
145Y ALA* 4.5 13.2 - - + -
147Y THR* 3.8 31.4 - - + +
151Y LEU* 3.7 27.1 - - + -
155Y VAL* 3.8 4.9 - - + -
159Y ALA* 3.5 25.8 - - + -
175Y CYS* 6.2 0.2 - - - -
189Y ILE* 4.2 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 121 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342X GLY* 4.3 17.5 + - - -
344X ARG* 4.8 8.0 + - - -
119Y TYR* 3.6 37.6 - + + -
120Y ILE* 1.3 81.4 - - - +
122Y GLU* 1.3 80.3 + - - +
124Y LEU* 3.4 6.0 + - - +
125Y LYS* 2.9 32.0 + - + +
155Y VAL* 3.6 25.7 - - + +
158Y TYR* 3.7 48.8 - + + +
159Y ALA* 3.8 6.7 - - - +
162Y GLU* 3.8 9.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 122 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344X ARG* 2.9 27.6 + - - -
659X ARG* 5.7 3.7 + - - +
87Y SER 5.3 2.9 - - - +
88Y GLN* 5.0 4.4 + - - +
89Y ALA* 3.3 31.0 - - + +
119Y TYR* 2.9 27.8 + - + +
121Y HIS* 1.3 99.0 + - - +
123Y GLY* 1.3 61.2 + - - +
125Y LYS* 3.6 27.8 + - - +
126Y LEU* 3.3 20.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 123 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48Y VAL* 3.9 15.0 - - - +
83Y ILE* 3.8 29.7 - - - +
85Y PHE* 4.3 6.2 - - - +
89Y ALA* 3.7 5.3 - - - +
119Y TYR 3.6 4.4 + - - -
120Y ILE 3.0 8.2 + - - -
122Y GLU* 1.3 75.7 - - - +
124Y LEU* 1.3 62.9 + - - +
125Y LYS 3.2 0.2 - - - -
126Y LEU* 3.3 2.8 + - - +
127Y ALA* 3.2 17.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 124 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48Y VAL* 4.4 9.2 - - + -
120Y ILE* 3.0 29.1 + - + +
121Y HIS* 4.1 1.1 - - - +
123Y GLY* 1.3 73.4 - - - +
125Y LYS* 1.3 57.2 + - - +
127Y ALA* 3.2 7.6 + - - +
128Y ASN* 2.8 35.7 + - - +
143Y ILE* 3.9 33.7 - - + -
145Y ALA* 4.8 7.2 - - + -
159Y ALA* 3.8 28.9 - - + +
162Y GLU* 3.6 22.4 - - + -
163Y ALA* 4.2 6.3 - - - +
166Y SER* 4.9 3.4 - - - +
173Y VAL* 4.6 12.1 - - + -
189Y ILE* 4.5 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 125 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344X ARG* 4.1 17.4 - - - +
121Y HIS* 2.9 17.8 + - + +
122Y GLU* 3.6 32.6 + - - +
123Y GLY 3.2 0.2 - - - -
124Y LEU* 1.3 77.0 - - - +
126Y LEU* 1.3 59.5 + - - +
128Y ASN* 3.2 3.5 + - + +
129Y GLU* 2.9 54.8 + - + +
162Y GLU* 3.5 29.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 126 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83Y ILE* 4.0 12.8 - - + -
89Y ALA* 3.6 40.8 - - + +
90Y THR* 3.7 5.2 - - - +
91Y ILE* 3.9 32.1 - - + +
122Y GLU 3.3 9.1 + - - +
123Y GLY 3.3 7.4 + - - +
124Y LEU 3.3 0.2 - - - -
125Y LYS* 1.3 81.1 - - + +
127Y ALA* 1.3 61.6 + - - +
129Y GLU* 3.7 23.8 + - + +
130Y GLN* 3.3 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 127 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46Y TYR* 4.1 12.2 - - + -
48Y VAL* 4.2 5.2 - - + -
83Y ILE* 3.4 20.2 - - + +
123Y GLY 3.2 8.8 + - - +
124Y LEU* 3.3 11.4 - - - +
126Y LEU* 1.3 76.3 - - - +
128Y ASN* 1.3 57.8 + - - +
130Y GLN* 3.3 4.9 + - - +
131Y ILE* 2.9 33.8 + - - +
143Y ILE* 3.9 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 128 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124Y LEU 2.8 18.1 + - - +
125Y LYS* 3.5 4.3 - - + +
127Y ALA* 1.3 68.0 - - - +
129Y GLU* 1.3 55.8 + - + +
131Y ILE* 3.2 10.2 + - - +
132Y GLN* 2.8 39.2 + - - +
143Y ILE* 3.7 5.7 - - - +
162Y GLU* 2.9 52.7 + - - +
165Y ILE* 3.5 13.7 - - + +
166Y SER* 2.4 29.0 + - - -
169Y LEU* 3.9 13.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 129 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125Y LYS* 2.9 49.1 + - + +
126Y LEU* 3.8 23.0 - - + +
127Y ALA 3.4 0.2 - - - -
128Y ASN* 1.3 73.0 - - + +
130Y GLN* 1.3 63.7 + - + +
132Y GLN* 3.3 13.5 + - - +
133Y LYS* 3.0 25.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 130 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46Y TYR* 3.5 25.4 + - + +
81Y SER* 2.9 21.4 + - - -
83Y ILE* 4.1 7.3 - - - +
91Y ILE* 4.0 23.4 - - + +
94Y PRO* 3.5 7.8 - - - +
95Y LEU* 2.7 34.2 + - + +
126Y LEU 3.3 15.6 + - - +
127Y ALA 3.3 6.5 + - - +
129Y GLU* 1.3 78.1 - - + +
131Y ILE* 1.3 57.3 + - - +
133Y LYS* 3.5 12.0 + - + +
134Y ALA* 3.0 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 131 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46Y TYR* 3.4 34.5 - - + -
127Y ALA 2.9 25.7 + - - +
128Y ASN* 3.2 12.1 + - - +
130Y GLN* 1.3 75.7 - - - +
132Y GLN* 1.3 61.8 + - - +
134Y ALA* 2.9 16.2 + - - +
136Y GLY* 3.2 23.9 + - - +
139Y THR* 4.5 0.7 - - - +
141Y SER* 3.8 15.7 - - - +
143Y ILE* 4.0 23.1 - - + -
169Y LEU* 4.2 31.6 - - + +
171Y ALA* 4.1 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 132 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128Y ASN* 2.8 18.7 + - - +
129Y GLU* 3.3 18.1 + - - +
131Y ILE* 1.3 74.0 - - - +
133Y LYS* 1.3 61.9 + - - +
134Y ALA 3.3 0.3 + - - -
135Y GLY* 3.5 9.9 + - - -
136Y GLY* 3.7 11.5 + - - -
165Y ILE* 6.1 1.0 - - - +
169Y LEU* 4.7 21.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 133 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129Y GLU 3.0 14.5 + - - +
130Y GLN* 3.9 9.6 - - - +
132Y GLN* 1.3 78.6 - - + +
134Y ALA* 1.3 60.7 + - - +
135Y GLY 3.3 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 134 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44Y ASP* 4.4 1.1 - - - +
46Y TYR* 4.2 9.2 - - - +
79Y ARG* 4.3 20.3 + - - +
95Y LEU* 4.4 7.0 - - + -
130Y GLN 3.0 16.4 + - - +
131Y ILE* 2.9 12.3 + - - +
133Y LYS* 1.3 76.9 - - - +
135Y GLY* 1.3 55.2 + - - +
136Y GLY 3.7 0.7 - - - -
138Y LYS* 4.0 10.2 - - - -
139Y THR* 3.6 21.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 135 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132Y GLN 3.5 6.1 + - - -
133Y LYS 3.3 4.8 + - - -
134Y ALA* 1.3 78.2 - - - +
136Y GLY* 1.3 64.1 + - - +
137Y LEU 3.4 1.4 + - - -
138Y LYS* 3.4 29.8 + - - +
139Y THR 4.9 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