Contacts of the helix formed by residues 257 - 267 (chain D) in PDB entry 5UH8
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 GLY 257 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128D ILE* 3.1 33.3 + - - +
129D ILE* 4.0 2.2 - - - -
131D PHE* 3.5 19.7 - - - -
256D MET* 1.3 74.2 - - - +
258D ALA* 1.3 65.2 + - - +
259D GLU 3.2 2.7 - - - -
260D SER* 2.2 28.3 + - - -
261D ILE* 3.6 3.3 + - - +
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Residues in contact with ALA 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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100D PRO* 3.4 21.8 - - + +
101D VAL* 3.8 3.4 - - - -
102D THR* 3.6 24.1 - - + +
129D ILE* 3.8 13.3 + - + +
131D PHE* 4.3 4.9 - - + -
257D GLY* 1.3 72.0 - - - -
259D GLU* 1.3 61.2 + - - +
261D ILE* 3.2 9.4 + - - +
262D GLN* 3.2 17.2 + - - +
313D VAL* 4.3 2.6 - - + +
375D GLN* 3.4 25.4 - - + +
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Residues in contact with GLU 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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99D ALA* 4.5 3.1 - - + +
100D PRO* 3.8 36.9 + - + +
131D PHE* 5.3 1.2 - - + -
255D ALA* 6.3 1.3 - - + -
256D MET 4.6 12.7 - - - +
257D GLY* 5.2 0.2 - - - -
258D ALA* 1.3 78.1 - - - +
260D SER* 1.3 66.0 + - - +
261D ILE 3.3 0.2 - - - -
262D GLN* 3.2 25.4 - - - +
263D LYS* 3.3 8.1 + - - +
371D LYS* 2.9 37.6 + - - +
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Residues in contact with SER 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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128D ILE* 3.8 6.9 - - - +
135D VAL* 4.1 6.7 - - - -
137D THR* 4.0 8.2 - - - +
255D ALA* 3.5 33.4 - - - -
256D MET* 3.3 7.3 - - - -
257D GLY 2.2 40.4 + - - -
259D GLU* 1.3 78.0 - - - +
261D ILE* 1.3 57.3 + - - +
263D LYS* 3.0 21.0 + - - +
264D LEU* 3.2 17.7 + - - +
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Residues in contact with ILE 261 (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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102D THR* 4.8 2.7 - - + -
114D LEU* 3.7 25.8 - - + -
118D LEU* 3.9 15.9 - - + -
120D LEU* 5.5 2.0 - - + -
125D LEU* 3.5 25.1 - - + -
128D ILE* 3.7 25.6 - - + -
129D ILE* 3.5 33.7 - - + -
135D VAL* 5.6 0.4 - - + -
257D GLY 3.8 5.2 - - - +
258D ALA 3.5 8.1 - - - +
260D SER* 1.3 72.9 - - - +
262D GLN* 1.3 65.8 + - - +
264D LEU* 3.2 10.0 + - + +
265D ILE* 3.1 26.5 + - + +
313D VAL* 4.9 2.7 - - + -
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Residues in contact with GLN 262 (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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100D PRO* 3.7 16.0 - - - +
258D ALA 3.2 3.8 + - - -
259D GLU* 3.2 17.6 - - - +
260D SER 3.1 0.2 - - - -
261D ILE* 1.3 78.9 - - - +
263D LYS* 1.3 60.2 + - - +
265D ILE* 3.4 6.7 + - - +
266D GLU* 3.1 21.9 + - + +
310D MET* 4.0 17.9 - - + +
313D VAL* 3.4 39.9 + - + +
315D ASP* 2.8 32.0 + - - +
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Residues in contact with LYS 263 (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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137D THR* 4.3 21.9 - - + +
138D SER* 4.7 14.5 + - - -
253D THR* 5.0 10.3 + - + +
259D GLU 3.3 6.1 + - - +
260D SER* 3.0 14.4 + - - +
262D GLN* 1.3 77.5 - - - +
264D LEU* 1.3 65.2 + - - +
266D GLU* 3.1 25.3 + - - +
267D ASN* 2.9 54.0 + - - +
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Residues in contact with LEU 264 (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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118D LEU* 3.9 20.9 - - + -
120D LEU* 5.5 4.5 - - + -
135D VAL* 4.7 11.9 - - + -
136D ILE 4.3 4.5 - - - +
137D THR* 4.0 35.2 - - + +
231D PRO* 4.7 4.9 - - + -
232D LYS* 3.7 43.5 - - + +
260D SER 3.2 17.6 + - - +
261D ILE* 3.2 12.1 + - - +
263D LYS* 1.3 80.6 - - - +
265D ILE* 1.3 62.8 + - - +
267D ASN* 3.3 7.5 + - + +
268D PHE* 3.1 23.7 + - + +
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Residues in contact with ILE 265 (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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114D LEU* 4.0 23.6 - - + -
117D LEU* 5.0 3.6 - - + -
118D LEU* 4.3 18.8 - - + -
261D ILE* 3.1 20.1 + - + +
262D GLN* 3.7 6.5 - - - +
264D LEU* 1.3 76.1 - - - +
266D GLU* 1.3 62.9 + - - +
268D PHE* 3.3 23.4 + - + +
309D PRO* 3.8 42.9 - - + +
310D MET* 3.7 22.6 - - + +
312D MET* 4.9 2.5 - - + -
313D VAL* 4.2 22.9 - - + -
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Residues in contact with GLU 266 (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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262D GLN* 3.1 12.7 + - + +
263D LYS* 3.1 30.4 + - - +
265D ILE* 1.3 81.0 - - - +
267D ASN* 1.3 68.3 + - - +
268D PHE 3.0 7.3 + - - +
310D MET* 3.7 19.3 - - + +
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Residues in contact with ASN 267 (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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137D THR 4.8 8.4 - - - +
138D SER* 5.2 4.9 - - - -
263D LYS* 2.9 48.7 + - - +
264D LEU* 3.3 7.5 + - + +
266D GLU* 1.3 86.4 - - - +
268D PHE* 1.3 58.7 + - - +
269D ASP 3.8 2.3 + - - -
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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
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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