Contacts of the helix formed by residues 246 - 256 (chain A) in PDB entry 1H3F
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 PRO 246 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244A THR 3.6 3.5 - - - +
245A GLU* 1.3 87.6 - - + +
247A PRO* 1.3 76.9 - - + +
248A GLU* 4.6 11.2 - - + +
249A ALA* 2.9 29.3 + - + +
250A MET 3.0 10.0 + - - -
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Residues in contact with PRO 247 (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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245A GLU 3.4 4.0 - - - +
246A PRO* 1.3 86.0 - - + +
248A GLU* 1.3 62.8 + - - +
250A MET* 3.2 3.8 + - + +
251A PHE* 2.9 27.2 + - - +
297A THR* 3.6 21.6 - - + +
301A ALA* 4.0 20.6 - - + -
334A GLU* 3.7 43.1 - - + +
338A ALA* 3.8 3.1 - - + -
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Residues in contact with GLU 248 (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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246A PRO* 3.1 11.8 + - + +
247A PRO* 1.3 79.4 - - - +
249A ALA* 1.3 80.1 + - + +
251A PHE* 3.8 1.4 - - - +
252A LYS* 3.1 41.8 + - - +
338A ALA* 3.6 21.4 - - - +
341A ARG* 3.3 46.2 - - + +
342A TYR* 5.7 0.7 - - - +
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Residues in contact with ALA 249 (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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245A GLU* 3.9 17.9 - - - +
246A PRO* 2.9 28.1 + - + +
248A GLU* 1.3 90.2 - - - +
250A MET* 1.3 65.9 + - - +
252A LYS* 3.6 5.5 - - - +
253A LYS* 3.1 31.9 + - - +
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Residues in contact with MET 250 (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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53A LEU* 5.0 7.0 - - + -
241A ILE* 3.9 21.8 - - + -
242A GLY 3.2 27.6 - - - +
243A LEU* 3.8 19.3 - - - +
245A GLU* 4.6 11.1 - - + +
246A PRO 3.0 11.2 + - - +
247A PRO* 3.8 9.6 - - + +
249A ALA* 1.3 74.0 - - - +
251A PHE* 1.3 60.7 + - - +
253A LYS* 3.3 3.2 + - - +
254A LEU* 2.9 47.8 + - + +
296A LEU* 3.7 26.9 - - - +
297A THR* 3.8 11.9 - - - +
300A TYR* 3.8 19.1 - - + -
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Residues in contact with PHE 251 (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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247A PRO 2.9 16.9 + - - +
248A GLU 3.8 4.0 - - - +
250A MET* 1.3 78.3 - - - +
252A LYS* 1.3 62.5 + - - +
254A LEU* 3.3 2.3 + - - +
255A MET* 3.0 55.2 + - + +
290A ARG* 4.5 3.1 - - - -
293A ALA* 3.6 28.7 - - + +
294A ARG* 4.0 11.4 - - + -
297A THR* 3.4 25.0 + - + +
335A VAL* 4.4 5.6 - - + -
338A ALA* 4.0 13.5 - - + +
339A GLU* 3.5 54.7 - - + -
342A TYR* 4.0 19.1 - + + -
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Residues in contact with LYS 252 (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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248A GLU* 3.1 33.2 + - - +
249A ALA* 3.6 7.4 - - - +
251A PHE* 1.3 76.6 - - - +
253A LYS* 1.3 62.4 + - + +
255A MET* 3.3 10.9 + - - +
256A ARG* 3.4 58.5 + - - +
342A TYR* 4.1 24.4 - - + +
345A VAL* 3.8 23.3 - - + +
431A SER 6.0 0.2 + - - -
432A ASP* 5.8 4.6 + - - -
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Residues in contact with LYS 253 (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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227A LEU* 4.3 15.4 - - + +
240A TYR* 3.6 26.3 + - - +
241A ILE* 3.8 21.5 - - + -
245A GLU* 2.9 41.2 + - - +
249A ALA* 3.1 20.2 + - - +
250A MET 3.7 3.6 - - - +
252A LYS* 1.3 78.7 - - + +
254A LEU* 1.3 63.7 + - - +
256A ARG* 3.0 18.2 + - - +
257A VAL* 3.4 11.8 + - - +
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Residues in contact with LEU 254 (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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53A LEU* 4.0 15.5 - - + -
241A ILE* 3.7 20.6 - - + -
250A MET* 2.9 35.5 + - + +
251A PHE 3.7 3.8 - - - +
253A LYS* 1.3 70.6 - - - +
255A MET* 1.3 62.1 + - - +
256A ARG 2.9 6.1 + - - -
257A VAL* 3.2 26.2 + - + +
265A TYR* 4.8 2.9 - - + -
289A HIS* 3.2 11.6 + - - -
292A LEU* 4.1 12.9 - - + +
293A ALA* 3.7 27.8 - - + +
296A LEU* 3.6 36.8 - - + -
297A THR* 3.9 5.4 - - - +
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Residues in contact with MET 255 (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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251A PHE* 3.0 45.0 + - + +
252A LYS 3.6 6.5 - - - +
253A LYS 3.3 0.2 - - - -
254A LEU* 1.3 76.2 - - - +
256A ARG* 1.3 59.6 + - - +
257A VAL 3.5 0.2 - - - -
286A VAL* 4.6 8.7 - - + +
289A HIS* 3.3 56.6 + - + +
290A ARG* 3.6 33.4 - - + +
293A ALA* 3.9 1.8 - - + -
342A TYR* 3.5 45.3 + - + +
505A SO4 4.8 0.7 + - - -
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Residues in contact with ARG 256 (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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227A LEU* 5.2 4.2 - - - +
252A LYS* 3.4 50.9 + - - +
253A LYS* 3.0 13.3 + - - +
254A LEU 2.9 1.6 - - - -
255A MET* 1.3 80.0 - - + +
257A VAL* 1.3 63.5 + - - +
258A PRO* 3.5 6.6 - - - +
342A TYR* 4.2 5.7 - - - -
345A VAL* 4.2 15.2 + - - +
347A LYS* 5.1 1.0 - - - +
505A SO4 2.8 48.6 + - - +
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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