Contacts of the helix formed by residues 112 - 131 (chain A) in PDB entry 1T2E
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 LEU 112 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A PHE 3.5 14.4 - - - +
101A THR 3.3 31.2 - - - +
102A LYS* 3.5 25.8 - - - +
103A ALA* 3.6 5.2 - - + +
107A TRP* 4.3 7.6 - - + +
108A ASN 4.2 6.3 - - - +
109A ARG* 3.3 19.5 - - + +
110A ASP 3.0 1.4 - - - -
111A ASP* 1.3 79.7 - - - +
113A LEU* 1.3 59.1 + - - +
114A PRO 3.4 0.2 - - - -
115A LEU* 2.9 28.7 + - + +
116A ASN* 3.1 29.1 + - - +
140A ASN* 3.7 16.4 - - + +
141A PRO* 4.3 0.7 - - - -
336A NAI 3.7 15.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A ASP 3.1 12.0 + - - +
112A LEU* 1.3 77.1 - - - +
114A PRO* 1.1 77.7 - - + +
115A LEU 2.8 1.7 + - - -
116A ASN* 3.2 7.2 + - - -
117A ASN* 2.6 30.7 + - - +
141A PRO* 3.8 20.1 - - + +
144A VAL* 4.6 0.4 - - + -
145A MET* 4.3 8.5 - - + -
325A MET* 3.4 50.0 - - + +
328A LEU* 3.5 29.8 - - + +
329A ALA* 3.7 12.3 - - + +
331A HIS 4.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A ASP 3.9 2.0 - - - +
111A ASP* 3.3 21.1 - - - +
112A LEU 3.5 0.2 - - - -
113A LEU* 1.1 107.8 - - + +
115A LEU* 1.3 67.0 + - + +
117A ASN* 2.9 27.0 + - - +
118A LYS* 5.6 0.5 - - - +
331A HIS 5.4 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A PHE* 3.5 30.9 - - + -
102A LYS 3.9 6.5 - - - +
103A PRO* 3.8 47.1 - - + -
111A ASP 3.9 15.5 - - - +
112A LEU* 2.9 18.3 + - + +
114A PRO* 1.3 91.9 - - + +
116A ASN* 1.3 58.6 + - - +
117A ASN* 3.7 0.7 - - - -
118A LYS* 5.2 2.3 + - - +
119A ILE* 3.4 19.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A ALA 5.1 0.2 - - - +
99A GLY* 3.1 8.1 - - - -
100A PHE* 2.8 49.3 + - - +
112A LEU* 3.1 18.6 + - - +
113A LEU 3.2 0.4 + - - +
115A LEU* 1.3 77.8 - - - +
117A ASN* 1.2 65.0 + - - +
118A LYS 3.3 2.5 - - - -
119A ILE* 3.2 9.1 + - - +
120A MET* 3.1 23.2 + - - +
139A THR* 3.5 25.7 - - + +
140A ASN 2.9 24.0 + - - +
145A MET* 4.1 7.0 - - - -
336A NAI 3.9 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A LEU* 2.6 30.1 + - + +
114A PRO* 2.9 27.4 + - - +
116A ASN* 1.2 78.1 - - - +
118A LYS* 1.3 87.7 + - - +
120A MET 3.2 10.9 + - - -
121A ILE* 3.3 13.4 + - + +
145A MET* 4.1 5.6 - - + -
148A LEU* 3.3 21.4 - - + +
329A ALA* 3.1 31.9 - - + +
331A HIS 3.4 20.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A PRO 5.6 0.7 - - - +
115A LEU 5.6 1.8 - - - +
116A ASN 5.2 0.4 - - - -
117A ASN* 1.3 89.3 + - - +
119A ILE* 1.3 67.3 + - + +
121A ILE* 3.5 18.9 + - + +
122A GLU* 3.2 23.2 + - - +
331A HIS 5.8 7.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A ALA* 3.7 23.3 - - + +
99A GLY* 4.0 13.9 - - - -
100A PHE* 3.9 17.0 - - + -
115A LEU 3.4 24.2 - - - +
116A ASN* 3.2 8.3 + - - +
117A ASN 3.2 0.2 - - - -
118A LYS* 1.3 78.0 - - + +
120A MET* 1.3 67.0 + - + +
122A GLU* 3.4 6.3 + - - +
123A ILE* 3.0 43.7 + - + +
336A NAI 3.7 25.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A VAL* 3.7 21.3 - - + -
98A ALA 3.6 11.2 - - - +
116A ASN 3.1 14.0 + - - +
117A ASN 3.2 6.2 + - - +
119A ILE* 1.3 84.7 - - + +
121A ILE* 1.3 58.6 + - - +
123A ILE* 4.5 2.7 - - + -
124A GLY 2.8 25.1 + - - -
137A VAL* 4.2 3.8 - - - -
139A THR* 3.5 33.7 - - + +
145A MET* 3.6 46.4 - - + +
148A LEU* 3.9 13.0 - - + -
149A LEU* 3.1 26.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ASN 3.3 17.2 + - - +
118A LYS* 3.7 20.9 - - + +
119A ILE 3.3 0.2 - - - -
120A MET* 1.3 77.6 - - - +
122A GLU* 1.3 67.0 + - - +
124A GLY* 3.7 0.9 - - - -
125A GLY* 3.0 19.4 + - - -
148A LEU* 4.0 14.1 - - + -
152A HIS* 3.6 49.5 - - + +
329A ALA 5.3 4.7 - - - +
330A HIS* 5.7 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A ILE* 5.5 1.7 - - - +
85A TYR* 2.9 33.1 + - - +
118A LYS 3.2 13.9 + - - +
119A ILE* 3.6 7.1 - - - +
121A ILE* 1.3 82.5 - - - +
123A ILE* 1.3 64.2 + - - +
125A GLY* 3.2 2.8 + - - -
126A HIS* 3.1 40.4 + - + -
336A NAI 4.1 5.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A VAL* 3.5 24.5 - - + -
85A TYR* 3.9 17.5 - - + +
88A LEU* 5.3 3.4 - - + -
96A VAL* 3.9 24.2 - - + -
98A ALA* 3.4 33.0 - - + -
119A ILE* 3.0 28.1 + - + +
120A MET* 4.0 4.7 - - + +
122A GLU* 1.3 79.7 - - - +
124A GLY* 1.3 59.4 + - - +
126A HIS* 3.0 8.4 + - - +
127A ILE* 2.7 47.5 + - + +
149A LEU* 4.2 3.8 - - + -
336A NAI 4.2 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A MET 2.8 12.5 + - - -
121A ILE 3.2 1.8 + - - -
123A ILE* 1.3 77.4 - - - +
125A GLY* 1.3 55.1 + - - +
127A ILE* 3.2 2.0 + - - +
128A LYS 2.9 24.8 + - - -
149A LEU* 2.9 27.4 - - - +
152A HIS* 3.4 8.9 - - - +
153A SER* 3.2 19.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ILE 3.0 13.6 + - - -
122A GLU* 3.7 3.4 - - - -
123A ILE 3.2 0.2 - - - -
124A GLY* 1.3 75.0 - - - +
126A HIS* 1.3 63.4 + - - +
128A LYS* 3.3 5.5 + - - +
129A LYS* 3.1 24.1 + - - +
152A HIS* 3.9 8.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A TYR* 3.1 56.6 - + + +
86A ASP* 4.5 5.6 + - - -
88A LEU* 3.8 19.3 - - + -
122A GLU* 3.1 30.7 + - + -
123A ILE 3.0 7.4 + - - +
125A GLY* 1.3 75.2 - - - +
127A ILE* 1.3 61.3 + - - +
129A LYS* 4.4 13.5 + - + -
130A ASN* 2.8 45.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A LEU* 4.3 5.6 - - + -
94A VAL* 4.0 16.6 - - + -
123A ILE* 2.7 39.1 + - + +
124A GLY 3.2 6.0 + - - +
126A HIS* 1.3 72.8 - - - +
128A LYS* 1.3 62.9 + - - +
131A CYS* 2.8 60.6 + - - +
135A ILE* 3.9 36.3 - - + -
149A LEU* 4.3 12.3 - - + -
153A SER* 3.9 15.7 - - - -
155A VAL* 4.1 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A GLY 2.9 14.7 + - - +
125A GLY* 3.6 6.3 - - - +
127A ILE* 1.3 80.3 - - - +
129A LYS* 1.3 62.2 + - - +
132A PRO* 3.6 23.2 - - + +
151A GLN 5.8 1.2 + - - -
152A HIS 4.1 12.0 + - - +
153A SER 3.3 24.9 + - - +
154A GLY* 4.7 11.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A ASP* 3.0 33.9 + - - -
125A GLY 3.1 14.5 + - - +
126A HIS* 3.7 17.7 + - + +
128A LYS* 1.3 83.6 - - - +
130A ASN* 1.3 72.9 + - - +
132A PRO* 4.2 3.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A TYR 3.9 8.9 + - - -
86A ASP* 3.4 45.3 + - - +
88A LEU* 3.7 17.3 - - + -
89A ALA* 3.4 25.9 - - - +
90A GLY 3.7 3.3 + - - -
126A HIS* 2.8 33.7 + - - +
129A LYS* 1.3 97.2 - - - +
131A CYS* 1.3 59.7 + - - +
132A PRO* 3.5 4.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A LEU* 3.4 33.9 - - - +
90A GLY* 4.5 0.9 - - - +
91A ALA* 3.8 21.1 - - - +
94A VAL* 3.7 28.7 - - - -
127A ILE* 2.8 32.7 + - - +
130A ASN* 1.3 76.0 - - - +
132A PRO* 1.3 64.8 - - - +
133A ALA* 2.9 20.1 + - + +
----------------------------------------------------------
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