Contacts of the helix formed by residues 244 - 260 (chain D) in PDB entry 3T79
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 ARG 244 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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241D GLN* 4.1 23.7 + - - +
242D TYR 5.1 2.0 + - - +
243D PRO* 1.3 76.4 - - - +
245D GLU* 1.3 67.3 + - - +
246D LEU* 3.4 4.9 - - + +
247D THR* 3.4 19.5 - - - +
248D LEU* 3.5 6.8 + - - +
7F T 3.1 40.2 + - - +
8F T 2.0 56.4 + - - -
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Residues in contact with GLU 245 (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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153D PHE* 3.6 31.6 - - + -
243D PRO 3.8 1.2 + - - -
244D ARG* 1.3 69.6 - - - +
246D LEU* 1.3 67.8 + - - +
247D THR 3.2 0.2 + - - -
248D LEU* 3.3 2.3 + - - +
249D GLY* 2.9 19.4 + - - -
265D LYS* 3.1 23.9 + - - +
269D PHE* 3.5 27.1 - - + +
270D GLN* 5.5 2.1 + - - -
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Residues in contact with LEU 246 (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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244D ARG* 3.4 3.8 - - + +
245D GLU* 1.3 80.1 - - - +
247D THR* 1.3 66.6 + - - +
249D GLY* 3.1 5.0 + - - -
250D ASN* 2.8 36.4 + - + +
265D LYS* 6.0 2.5 - - - +
6E T 4.9 20.0 - - + +
7E A 3.7 29.6 - - - +
8E T 5.7 2.9 - - + +
7F T 5.7 5.6 - - + -
8F T 4.5 17.3 - - + -
9F A 3.8 15.7 - - - +
10F T 4.5 3.1 - - - +
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Residues in contact with THR 247 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243D PRO* 5.0 7.9 - - + -
244D ARG* 3.4 14.2 + - - +
245D GLU 3.2 0.2 - - - -
246D LEU* 1.3 78.4 - - - +
248D LEU* 1.3 56.9 + - + +
250D ASN* 2.5 30.8 + - - +
251D TRP* 2.9 51.8 + - + +
6F T 3.6 22.2 - - - +
7F T 3.0 27.0 + - - +
8F T 6.1 0.7 - - - +
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Residues in contact with LEU 248 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138D LYS* 6.1 1.1 - - + -
139D LEU* 3.9 20.0 - - + +
142D ASP* 3.3 33.9 - - + +
153D PHE* 3.6 26.0 - - + -
234D ILE* 6.0 3.1 - - + -
242D TYR* 4.7 8.5 - - + -
243D PRO* 4.9 17.0 - - + -
244D ARG 3.5 6.2 + - - +
245D GLU 3.3 5.5 + - - +
247D THR* 1.3 78.7 - - - +
249D GLY* 1.3 56.0 + - - +
251D TRP* 2.7 46.5 + - + +
252D TYR* 2.9 18.3 + - + -
269D PHE* 3.6 15.0 - - + -
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Residues in contact with GLY 249 (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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245D GLU 2.9 13.4 + - - -
246D LEU* 3.3 7.9 - - - -
248D LEU* 1.3 76.8 - - - +
250D ASN* 1.3 53.3 + - - +
253D PRO* 2.9 22.2 - - - +
263D TYR* 4.0 9.8 + - - -
265D LYS* 4.4 12.5 - - - +
269D PHE* 3.3 18.9 - - - -
6E T 5.1 4.9 + - - -
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Residues in contact with ASN 250 (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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129D HIS* 5.8 2.7 - - - -
246D LEU* 2.8 22.5 + - + +
247D THR* 2.5 21.3 + - - +
249D GLY* 1.3 71.3 - - - -
251D TRP* 1.3 73.7 + - + +
253D PRO* 3.0 14.8 - - - +
254D THR* 2.4 26.2 + - - +
7E A 5.7 0.7 + - - -
8E T 5.4 10.5 - - - +
7F T 6.0 4.0 - - - +
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Residues in contact with TRP 251 (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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129D HIS* 3.6 24.5 - + + -
130D PHE* 3.1 36.7 - + + -
135D ASP* 5.7 1.4 - - - +
138D LYS* 6.2 3.9 - - + +
139D LEU* 3.1 21.8 - - + -
243D PRO* 6.3 0.2 - - - +
247D THR* 3.1 35.3 - - + +
248D LEU* 2.7 31.4 + - + +
250D ASN* 1.3 94.9 - - + +
252D TYR* 1.3 64.7 + - - +
254D THR* 2.3 29.9 + - - -
255D ILE* 3.1 4.3 + - - +
6F T 3.1 47.7 - - - -
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Residues in contact with TYR 252 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139D LEU* 4.2 19.7 - - + -
142D ASP* 3.0 24.5 + - - -
143D PHE* 2.9 55.4 - + + -
146D LYS* 5.3 0.7 - - - +
156D ARG* 4.8 0.5 + - - -
248D LEU* 2.9 19.8 + - + +
251D TRP* 1.3 78.2 - - - +
253D PRO* 1.3 71.7 - - + +
255D ILE* 2.8 18.2 + - + +
256D PHE* 2.7 45.7 - + - -
263D TYR* 3.5 19.1 - + + +
268D TRP* 4.1 20.2 - + + +
269D PHE* 3.7 22.2 - + - -
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Residues in contact with PRO 253 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249D GLY 2.9 27.8 - - - +
250D ASN* 3.0 24.5 - - - +
252D TYR* 1.3 82.4 - - + +
254D THR* 1.3 47.9 + - - +
256D PHE* 3.1 8.4 + - + +
257D LYS* 2.7 47.5 + - - +
263D TYR* 4.1 28.7 - - + -
6E T 5.3 8.7 - - - +
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Residues in contact with THR 254 (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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125D LEU* 5.3 5.7 - - + +
127D SER* 4.0 28.7 - - - +
129D HIS* 5.7 2.5 - - + +
130D PHE* 4.5 10.7 - - + -
250D ASN* 2.4 20.5 + - - +
251D TRP* 2.3 28.2 + - - -
253D PRO* 1.3 77.0 - - - +
255D ILE* 1.3 56.6 + - - -
257D LYS* 3.0 37.7 - - + +
258D TYR* 3.4 11.3 + - - +
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Residues in contact with ILE 255 (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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113D ILE* 4.4 10.3 - - + -
116D ASN* 5.0 2.9 - - + -
117D LEU* 3.7 36.8 - - + -
125D LEU* 5.1 8.3 - - + -
130D PHE* 4.9 7.3 - - + -
139D LEU* 3.7 25.1 - - + -
143D PHE* 6.1 0.7 - - + -
251D TRP 3.1 2.3 + - - +
252D TYR* 2.8 27.6 + - + +
254D THR* 1.3 78.7 - - - +
256D PHE* 1.3 74.0 - - + +
258D TYR* 3.3 17.6 - - + +
259D CYS* 2.9 45.2 + - - -
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Residues in contact with PHE 256 (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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109D ILE* 4.6 4.7 - - + -
113D ILE* 3.6 23.6 - - + -
143D PHE* 3.9 11.4 - + - -
252D TYR* 2.7 66.4 + + - -
253D PRO 3.1 5.6 + - - +
255D ILE* 1.3 79.1 - - + +
257D LYS* 1.3 55.3 + - - +
259D CYS* 2.9 5.4 + - - +
260D GLN 2.3 34.8 + - - -
261D LEU* 2.9 30.6 + - + +
262D PRO 3.5 20.4 - - - +
263D TYR* 3.6 20.2 - + + -
268D TRP* 3.8 25.4 - + - -
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Residues in contact with LYS 257 (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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253D PRO* 2.7 36.0 + - - +
254D THR* 3.0 38.1 - - + +
256D PHE* 1.3 70.4 - - - +
258D TYR* 1.3 55.1 + - - +
260D GLN* 2.5 34.3 + - - +
261D LEU 4.4 1.3 + - - -
7E A 5.8 2.2 + - - -
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Residues in contact with TYR 258 (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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116D ASN* 4.3 10.3 - - + -
119D ASN* 5.2 1.4 + - - -
121D SER 4.7 0.2 + - - -
122D THR* 3.7 20.4 - - + +
124D SER* 2.9 18.6 - - - -
125D LEU* 2.9 47.8 - - + -
254D THR 3.5 10.5 - - - +
255D ILE* 3.3 27.6 - - + +
256D PHE 3.3 0.2 - - - -
257D LYS* 1.3 83.5 - - - +
259D CYS* 1.3 61.9 + - - +
260D GLN* 4.3 4.7 + - - +
395D ILE* 2.9 51.2 - - + +
396D ASP* 2.4 28.9 + - - +
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Residues in contact with CYS 259 (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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112D LYS* 2.3 50.7 + - + +
113D ILE* 4.2 10.5 - - + -
116D ASN* 3.9 26.2 - - - -
255D ILE* 2.9 47.9 + - - +
256D PHE* 2.9 6.7 + - - +
258D TYR* 1.3 77.1 - - - +
260D GLN* 1.3 66.9 + - - +
261D LEU* 3.8 13.6 - - + +
395D ILE* 4.8 2.0 - - - -
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Residues in contact with GLN 260 (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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112A LYS* 5.9 0.2 - - - +
260A GLN* 2.5 44.2 + - - +
392A ALA 4.7 3.1 - - - +
393A GLN 6.0 0.5 - - - -
394A LEU 4.8 7.1 - - - +
395A ILE* 4.9 14.8 - - + +
112D LYS* 4.6 3.5 + - - +
256D PHE 2.3 17.1 + - - -
257D LYS* 2.5 20.2 + - - +
258D TYR 4.3 2.9 - - - +
259D CYS* 1.3 72.9 + - - +
261D LEU* 1.3 63.5 + - - +
395D ILE* 4.6 13.5 - - - +
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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
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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