Contacts of the helix formed by residues 305 - 317 (chain A) in PDB entry 5HAN
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 THR 305 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A LYS* 4.0 17.0 - - - +
124A MET 3.3 11.7 + - - +
125A TYR* 3.8 37.9 + - + +
296A THR* 3.7 8.1 - - - +
304A TYR* 1.3 80.8 - - - +
306A ALA* 1.3 59.7 + - - +
307A PHE* 3.6 10.3 + - - +
308A VAL* 3.2 24.3 + - - +
309A LEU* 3.1 22.3 + - - +
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Residues in contact with ALA 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A ARG* 3.9 23.5 + - - +
292A HIS* 5.2 1.1 - - + -
296A THR* 3.6 26.8 + - + +
305A THR* 1.3 71.8 - - - +
307A PHE* 1.3 60.3 + - - +
309A LEU* 3.6 4.6 - - - +
310A SER* 2.9 35.5 + - - -
323A THR 5.9 0.2 - - - +
337A ASP* 6.1 1.6 - - - +
340A ILE* 4.1 14.8 - - + -
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Residues in contact with PHE 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A TYR 3.8 15.5 - - - +
126A ASP* 3.4 22.4 - - - -
305A THR* 3.7 10.2 - - - +
306A ALA* 1.3 79.0 - - - +
308A VAL* 1.3 60.7 + - + +
310A SER* 3.4 1.7 + - - -
311A LYS* 3.0 37.3 + - + +
339A ALA* 4.1 11.0 - - + -
340A ILE* 3.8 35.3 - - + +
343A MET* 3.7 39.8 - - + +
350A ASP 4.5 1.3 - - - -
351A GLY* 3.4 27.8 - - - -
352A PRO* 3.8 13.2 - - + -
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Residues in contact with VAL 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A PHE* 5.3 0.4 - - + -
124A MET* 3.6 22.0 - - + +
125A TYR 3.5 33.2 - - - +
126A ASP* 3.7 9.4 - - - +
127A PHE* 3.8 23.1 - - + -
304A TYR* 3.6 25.8 - - + -
305A THR* 3.2 13.9 + - - +
307A PHE* 1.3 77.1 - - + +
309A LEU* 1.3 63.4 + - - +
311A LYS* 3.3 1.6 + - - +
312A MET* 3.0 34.9 + - + +
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Residues in contact with LEU 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266A TYR* 4.5 7.4 - - + -
287A TYR* 3.5 23.3 - - - +
289A ARG* 4.1 24.9 - - + +
292A HIS* 3.7 31.4 - - + +
296A THR* 4.4 6.5 - - + -
304A TYR* 3.9 25.1 - - + +
305A THR 3.1 13.2 + - - +
306A ALA* 3.6 9.6 - - - +
308A VAL* 1.3 78.2 - - - +
310A SER* 1.3 57.9 + - - +
312A MET* 3.4 15.7 + - + +
313A ALA* 3.0 26.5 + - - +
316A GLN* 5.0 1.7 - - - +
321A ILE* 4.7 7.0 - - + -
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Residues in contact with SER 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A ARG* 5.1 3.8 + - - -
306A ALA 2.9 18.1 + - - -
307A PHE 3.7 2.2 - - - -
309A LEU* 1.3 74.1 - - - +
311A LYS* 1.3 65.9 + - - +
313A ALA* 3.3 16.4 + - - +
314A ARG 3.3 9.2 + - - -
321A ILE* 4.4 14.9 - - - +
322A HIS 4.6 5.4 + - - -
323A THR* 4.4 7.4 - - - +
340A ILE* 3.3 30.1 - - - +
344A ILE* 3.5 20.2 - - - +
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Residues in contact with LYS 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A ASP* 4.0 4.8 + - - -
127A PHE* 2.7 54.2 + - + +
128A TYR* 4.4 0.2 - - - +
129A VAL* 4.8 1.3 - - - -
307A PHE* 3.0 28.5 + - + +
308A VAL* 3.3 4.7 + - - +
310A SER* 1.3 77.0 - - - +
312A MET* 1.3 62.8 + - - +
314A ARG* 3.4 12.5 + - - +
315A LEU* 3.5 13.3 + - - +
343A MET* 4.1 22.2 - - + +
344A ILE* 4.4 7.8 - - - +
354A PHE* 5.3 3.0 + - - +
356A GLN* 2.9 44.5 + - - +
358A TRP* 3.8 20.9 - - + -
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Residues in contact with MET 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A ILE* 4.0 20.8 - - + +
105A PHE* 3.7 17.7 - - + -
106A LEU* 3.5 35.2 - - + -
127A PHE* 3.7 21.5 - - + -
304A TYR* 3.9 20.2 - - + +
308A VAL* 3.0 29.9 + - + +
309A LEU* 3.7 20.4 - - + +
311A LYS* 1.3 75.2 - - - +
313A ALA* 1.4 57.3 + - - +
315A LEU* 3.1 7.7 + - - +
316A GLN* 2.9 38.8 + - - +
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Residues in contact with ALA 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287A TYR* 3.9 15.7 - - + -
309A LEU 3.0 8.9 + - - +
310A SER 3.3 7.6 + - - +
312A MET* 1.4 75.8 - - - +
314A ARG* 1.4 61.6 + - - +
316A GLN* 3.3 13.8 + - - +
317A GLY 3.0 6.4 + - - -
318A ALA* 3.0 31.1 + - + +
321A ILE* 3.4 36.6 - - + -
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Residues in contact with ARG 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A GLY* 3.5 1.6 - - - -
140A PRO* 3.4 19.6 - - - +
310A SER 3.3 9.1 + - - +
311A LYS 3.6 10.1 - - - +
312A MET 3.2 0.6 - - - -
313A ALA* 1.4 77.5 - - - +
315A LEU* 1.4 62.5 + - - +
317A GLY 3.2 9.5 + - - -
343A MET 2.9 25.5 + - - -
344A ILE* 3.2 32.3 + - + +
345A THR 4.4 0.2 + - - -
346A GLU 2.8 31.3 + - - -
347A ASP* 4.7 1.4 - - - +
358A TRP* 3.3 43.6 - - + +
361A MET* 2.9 27.2 + - - +
362A ASN 3.0 23.3 + - - +
363A PRO* 3.7 4.9 - - - +
364A THR* 3.4 23.2 + - - +
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Residues in contact with LEU 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A ILE* 4.3 15.0 - - + -
127A PHE* 4.0 31.2 - - + -
129A VAL* 4.5 9.2 - - + -
134A LEU* 3.3 34.3 - - + -
137A PHE* 3.5 40.1 - - + +
138A ASP 3.5 9.4 + - - -
139A GLY 2.9 22.9 + - - -
311A LYS 3.5 9.1 + - - +
312A MET 3.1 7.0 + - - +
314A ARG* 1.4 77.0 - - - +
316A GLN* 1.3 58.3 + - - +
358A TRP* 3.8 13.7 - - + -
361A MET* 4.1 6.7 - - - -
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Residues in contact with GLN 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A ILE* 3.8 28.2 - - + +
137A PHE* 5.5 1.6 - - - -
138A ASP* 4.1 8.4 - - - +
139A GLY 4.5 1.1 - - - -
265A GLY 5.7 0.2 + - - -
270A PRO* 3.6 35.3 + - - +
273A VAL* 3.9 27.8 - - + +
274A THR* 4.8 9.8 + - - +
277A ARG* 3.7 19.2 - - - +
287A TYR* 4.0 13.8 + - - -
309A LEU* 5.0 1.4 - - - +
312A MET* 2.9 28.8 + - - +
313A ALA* 3.5 18.9 + - - +
314A ARG 3.3 0.2 - - - -
315A LEU* 1.3 75.5 - - - +
317A GLY* 1.3 57.3 + - - +
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Residues in contact with GLY 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A GLY 3.3 29.4 - - - -
140A PRO* 3.5 8.2 - - - +
141A SER 4.5 0.2 + - - -
277A ARG* 3.6 18.6 - - - -
285A LEU* 3.8 10.6 - - - +
313A ALA 3.0 3.2 + - - -
314A ARG 3.2 4.3 + - - -
315A LEU 3.2 0.4 - - - -
316A GLN* 1.3 79.3 - - - +
318A ALA* 1.3 66.6 + - - +
319A SER* 3.3 3.8 + - - -
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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