Contacts of the helix formed by residues 138 - 154 (chain D) in PDB entry 1T9D
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 HIS 138 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138C HIS* 5.7 0.4 + - - -
140C GLN* 2.9 28.1 + - - -
555C MET* 3.4 44.4 - - + +
113D TYR* 5.2 0.7 - - - -
136D PRO* 3.4 8.3 - - - +
137D LYS* 1.3 80.7 - - - +
139D GLU* 1.3 59.2 + - - +
140D GLN* 2.9 43.6 + - + +
141D GLY* 2.7 30.1 + - - +
142D ALA 3.4 3.5 + - - -
169D ASN* 3.3 34.8 + - + -
558D THR* 4.8 4.9 - - + -
559D GLU* 3.2 11.6 + - - +
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Residues in contact with GLU 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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555C MET* 3.6 15.6 - - - +
113D TYR* 3.8 16.6 - - + +
136D PRO* 4.7 2.0 - - - +
138D HIS* 1.3 72.5 + - - +
140D GLN* 1.3 61.5 + - - +
142D ALA* 2.9 11.2 + - - +
143D GLY 2.9 19.1 + - - -
161D VAL* 3.6 19.1 - - + -
162D THR* 5.0 0.5 - - - +
166D GLY* 3.5 25.6 - - - +
169D ASN* 2.9 33.9 - - + +
170D VAL* 3.7 17.0 - - + +
3703D PYD 2.7 30.8 + - - +
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Residues in contact with GLN 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138C HIS* 2.8 33.9 + - - -
169C ASN* 4.1 9.2 + - - +
138D HIS* 2.9 24.2 + - + +
139D GLU* 1.3 77.5 - - - +
141D GLY* 1.3 57.9 + - - +
143D GLY* 3.2 1.4 + - - -
144D HIS* 2.9 59.8 + - - +
169D ASN 3.5 13.6 + - - +
172D THR* 4.1 11.8 - - - +
173D PRO* 3.7 18.5 - - + +
524D THR* 4.2 6.3 - - - +
525D MET 4.7 3.6 + - - -
556D THR* 4.3 16.3 - - + +
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Residues in contact with GLY 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138D HIS* 2.7 12.9 + - - +
140D GLN* 1.3 80.0 - - - +
142D ALA* 1.3 55.0 + - - -
144D HIS* 3.4 0.4 + - - -
145D MET* 2.8 41.7 + - - +
530D PRO* 3.7 13.0 - - - +
556D THR* 6.0 2.6 - - - +
559D GLU* 3.7 23.4 + - - -
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Residues in contact with ALA 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D PHE* 3.7 16.1 - - + +
112D GLY* 4.1 24.0 - - - +
136D PRO* 3.8 23.3 - - + +
138D HIS 3.4 3.8 + - - -
139D GLU* 2.9 13.8 + - - +
141D GLY* 1.3 75.8 - - - +
143D GLY* 1.3 57.3 + - - +
145D MET* 3.4 5.3 + - - +
146D ALA* 3.0 29.3 + - - +
159D VAL* 4.1 9.4 - - + +
161D VAL* 5.0 1.3 - - + -
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Residues in contact with GLY 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139D GLU 2.9 11.9 + - - -
140D GLN 3.6 3.1 - - - -
141D GLY 3.2 0.4 - - - -
142D ALA* 1.3 77.3 - - - +
144D HIS* 1.3 62.0 + - - +
146D ALA* 3.2 6.1 + - - +
147D GLU* 3.0 23.6 + - - +
159D VAL* 4.2 15.6 - - - +
170D VAL* 5.3 2.9 - - - -
173D PRO* 3.7 22.0 - - - -
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Residues in contact with HIS 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140D GLN* 2.9 52.7 + - + +
143D GLY* 1.3 72.4 - - - +
145D MET* 1.3 60.5 + - - +
147D GLU* 2.9 32.0 + - - +
148D GLY 3.0 22.9 + - - -
172D THR* 4.3 1.1 - - + -
173D PRO* 3.8 19.0 - - + +
176D ASP* 4.5 2.7 - - + -
524D THR* 3.7 23.3 - - + +
526D GLY 4.4 2.5 - - - -
527D TYR* 3.5 26.4 - + + -
530D PRO* 3.5 29.4 - - + -
531D ALA* 3.5 11.6 - - - +
556D THR* 4.9 1.8 - - + -
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Residues in contact with MET 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D PHE* 3.5 20.4 - - + -
134D VAL* 4.0 25.1 - - + -
136D PRO* 3.5 19.5 - - + -
141D GLY 2.8 24.4 + - - +
142D ALA* 3.6 2.7 - - - +
144D HIS* 1.3 76.7 - - - +
146D ALA* 1.3 58.6 + - - +
148D GLY 3.3 0.3 + - - -
149D TYR* 2.8 26.7 + - - +
530D PRO* 3.3 26.5 - - + +
533D ILE* 4.1 22.0 - - + -
534D GLY* 3.2 11.4 - - - -
559D GLU* 3.5 31.0 - - + +
562D SER* 4.0 14.8 - - - -
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Residues in contact with ALA 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111D PHE* 3.8 21.7 - - + -
142D ALA 3.0 15.0 + - - +
143D GLY 3.2 9.4 + - - +
145D MET* 1.3 78.0 - - - +
147D GLU* 1.3 56.7 + - + +
149D TYR* 3.3 1.9 + - - +
150D ALA* 2.9 30.3 + - - +
157D GLY* 3.7 17.5 - - - -
159D VAL* 3.6 22.0 - - + -
184D MET* 5.5 4.3 - - + -
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Residues in contact with GLU 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143D GLY 3.0 15.4 + - - +
144D HIS* 2.9 33.8 + - - +
145D MET 3.2 0.2 - - - -
146D ALA* 1.3 79.3 - - + +
148D GLY* 1.3 57.2 + - - +
150D ALA* 3.2 2.4 + - - +
151D ARG* 2.9 31.4 + - - +
173D PRO* 3.3 25.9 - - + +
176D ASP* 2.5 26.9 - - - +
177D ALA* 3.2 24.6 + - + -
182D ILE* 3.6 21.8 - - + +
527D TYR* 3.9 15.3 - - + +
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Residues in contact with GLY 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144D HIS 3.0 12.2 + - - -
145D MET 3.7 1.1 - - - -
147D GLU* 1.3 75.8 - - - +
149D TYR* 1.3 63.2 + - - +
152D ALA* 3.0 26.7 + - - +
517D ILE* 3.7 18.6 - - - +
527D TYR* 4.3 0.8 + - - -
531D ALA* 3.5 24.0 - - - -
535D ALA* 3.7 8.1 - - - -
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Residues in contact with TYR 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108D ASP* 2.7 32.4 + - - -
109D THR* 3.7 25.9 + - - -
111D PHE* 3.6 22.2 - + + -
145D MET 2.8 17.7 + - - +
146D ALA 3.5 3.8 - - - +
148D GLY* 1.3 76.1 - - - +
150D ALA* 1.3 61.0 + - - +
152D ALA 3.3 0.7 + - - -
153D SER* 2.9 48.9 + - - -
155D LYS* 3.7 16.5 + - + +
156D PRO 4.0 13.9 - - - -
157D GLY* 4.3 12.8 - - - -
534D GLY 3.4 14.9 - - - +
537D VAL* 4.3 3.6 - - + -
538D ALA* 3.5 37.6 - - + +
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Residues in contact with ALA 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146D ALA 2.9 17.2 + - - +
147D GLU 3.7 3.8 - - - +
149D TYR* 1.3 73.8 - - - +
151D ARG* 1.3 62.0 + - - +
154D GLY* 2.9 30.5 + - - -
155D LYS 3.1 26.0 - - - +
157D GLY 3.7 2.9 - - - +
182D ILE* 3.9 11.4 - - + -
183D PRO* 3.5 28.0 - - + +
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Residues in contact with ARG 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147D GLU 2.9 16.8 + - - +
148D GLY 4.0 3.1 - - - +
150D ALA* 1.3 77.1 - - - +
152D ALA* 1.3 59.6 + - - +
154D GLY* 4.6 1.8 + - - -
182D ILE* 4.8 14.3 - - + +
183D PRO* 6.3 0.2 - - - -
514D HIS* 4.0 24.1 + - - +
517D ILE* 4.0 28.9 - - + +
527D TYR* 5.1 0.2 - - - +
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Residues in contact with ALA 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148D GLY 3.0 17.8 + - - +
149D TYR 3.9 2.0 - - - +
151D ARG* 1.3 78.8 - - - +
153D SER* 1.3 58.9 + - - +
492D ILE* 4.3 12.9 - - + +
514D HIS* 4.6 15.6 - - - +
517D ILE* 3.7 15.0 - - + -
535D ALA* 3.9 20.2 - - + +
538D ALA* 4.1 7.0 - - + -
539D LYS* 3.3 21.6 - - + +
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Residues in contact with SER 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149D TYR* 2.9 30.4 + - - -
152D ALA* 1.3 78.8 - - - +
154D GLY* 1.3 57.0 + - - +
155D LYS* 3.1 39.8 + - - +
538D ALA* 3.8 18.4 - - - -
539D LYS* 4.6 9.0 + - - +
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Residues in contact with GLY 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150D ALA 2.9 14.7 + - - -
151D ARG 4.6 1.4 + - - -
152D ALA 3.7 0.6 - - - -
153D SER* 1.3 79.0 - - - +
155D LYS* 1.3 60.9 + - - +
156D PRO* 4.3 1.4 - - - +
183D PRO* 5.1 5.8 - - - +
238D THR* 6.0 0.5 - - - +
514D HIS* 6.1 5.1 + - - -
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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) + - + + + + + -
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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