Contacts of the helix formed by residues 332 - 346 (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 332 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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298A ALA* 4.9 0.7 - - + -
317A LEU* 3.5 34.9 - - + +
319A TYR* 4.3 1.8 - - + +
331A GLY* 1.3 85.6 - - - +
333A GLU* 1.3 60.9 + - - +
334A GLU* 4.5 5.4 - - + +
335A VAL* 3.2 32.1 + - + +
336A ARG* 2.9 26.0 + - - +
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Residues in contact with GLU 333 (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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331A GLY 5.0 2.3 - - - +
332A PRO* 1.3 73.9 - - - +
334A GLU* 1.3 56.9 + - - +
336A ARG* 3.4 36.8 + - - -
337A ARG* 2.8 63.2 + - + +
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Residues in contact with GLU 334 (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* 3.7 29.3 - - + +
301A ALA* 3.7 31.6 - - + +
302A LEU* 6.1 0.9 - - - +
332A PRO* 3.2 4.9 - - + +
333A GLU* 1.3 77.6 - - - +
335A VAL* 1.3 63.8 + - + +
337A ARG* 4.2 3.9 - - - +
338A ALA* 3.3 21.7 + - - +
341A ARG* 5.3 0.9 + - - -
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Residues in contact with VAL 335 (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* 4.4 13.9 - - + -
294A ARG* 4.2 22.4 - - + +
297A THR* 4.5 8.1 - - + +
298A ALA* 3.6 33.9 - - + +
301A ALA* 5.5 1.8 - - + -
319A TYR* 3.2 23.1 - - + +
332A PRO* 3.2 25.6 + - + +
334A GLU* 1.3 77.5 - - + +
336A ARG* 1.3 66.0 - - - +
338A ALA* 3.1 5.5 + - - +
339A GLU* 2.9 23.1 + - - +
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Residues in contact with ARG 336 (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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319A TYR* 4.5 2.1 + - - -
328A LYS 4.0 15.6 - - - +
329A GLU* 3.0 48.6 + - - +
330A ALA 4.0 10.3 - - - +
331A GLY 4.7 2.5 - - - -
332A PRO 2.9 17.8 + - - +
333A GLU* 3.4 35.0 + - - +
335A VAL* 1.3 78.7 - - - +
337A ARG* 1.3 61.5 + - + +
339A GLU* 3.5 6.5 + - - +
340A ALA* 3.1 26.5 + - + +
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Residues in contact with ARG 337 (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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333A GLU* 2.8 46.2 + - - +
334A GLU* 4.2 4.3 - - - +
336A ARG* 1.3 75.3 - - + +
338A ALA* 1.3 61.0 + - - +
340A ALA* 3.3 7.6 + - - +
341A ARG* 2.9 59.9 + - - +
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Residues in contact with ALA 338 (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* 3.8 10.1 - - + +
248A GLU* 3.6 39.8 - - - +
251A PHE* 4.0 13.9 - - + +
297A THR* 4.5 0.9 - - + -
334A GLU 3.3 13.8 + - - +
335A VAL* 3.1 12.0 + - - +
337A ARG* 1.3 78.6 - - - +
339A GLU* 1.3 61.5 + - - +
341A ARG* 3.3 6.1 + - - +
342A TYR* 3.1 21.3 + - - +
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Residues in contact with GLU 339 (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* 3.5 32.9 - - + -
290A ARG* 2.9 28.5 + - - +
294A ARG* 2.9 45.3 + - - +
319A TYR* 4.4 5.0 + - - -
328A LYS* 2.9 21.6 - - + +
335A VAL 2.9 14.2 + - - +
336A ARG* 3.8 5.3 - - - +
338A ALA* 1.3 74.8 - - - +
340A ALA* 1.3 61.5 + - - +
342A TYR* 3.3 2.9 + - - +
343A ASP* 3.0 32.9 + - - +
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Residues in contact with ALA 340 (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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336A ARG* 3.1 18.6 + - + +
337A ARG* 3.6 9.0 - - - +
339A GLU* 1.3 75.8 - - - +
341A ARG* 1.3 62.2 + - + +
343A ASP* 3.3 9.4 + - - +
344A GLU* 2.9 32.9 + - + +
413A SER 4.5 0.7 - - - +
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Residues in contact with ARG 341 (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* 3.3 42.9 - - + +
334A GLU 5.3 0.6 + - - -
337A ARG* 2.9 65.6 + - - +
338A ALA* 3.6 9.0 - - - +
339A GLU 3.3 0.2 - - - -
340A ALA* 1.3 77.0 - - + +
342A TYR* 1.3 63.0 + - - +
344A GLU* 3.3 30.9 + - - +
345A VAL* 3.6 13.3 + - - +
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Residues in contact with TYR 342 (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 5.7 0.7 - - - +
251A PHE* 4.0 14.6 - + + -
252A LYS* 4.1 29.4 - - + +
255A MET* 3.5 51.6 + - + +
256A ARG* 4.2 12.8 - - - -
290A ARG* 4.3 6.1 - - - -
338A ALA 3.1 12.2 + - - +
339A GLU 3.4 7.6 - - - +
341A ARG* 1.3 78.4 - - - +
343A ASP* 1.3 68.5 + - - +
345A VAL* 3.1 7.7 + - + +
346A ALA* 2.8 47.8 + - + +
505A SO4 2.9 35.9 + - - -
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Residues in contact with ASP 343 (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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290A ARG* 2.9 27.2 + - - -
328A LYS* 3.2 35.8 + - - +
339A GLU* 3.0 22.3 + - - +
340A ALA* 3.3 9.1 + - - +
342A TYR* 1.3 82.5 - - - +
344A GLU* 1.3 61.3 + - - +
346A ALA* 3.9 10.7 + - - +
413A SER 3.4 14.4 - - - +
414A ARG* 3.5 5.1 - - + +
415A PRO* 3.4 14.2 - - - +
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Residues in contact with GLU 344 (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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340A ALA* 2.9 25.7 + - - +
341A ARG* 3.4 23.2 - - - +
342A TYR 3.1 0.6 - - - -
343A ASP* 1.3 80.1 - - - +
345A VAL* 1.3 64.5 + - + +
412A LEU 4.0 9.1 - - - +
413A SER* 3.4 21.5 - - - +
414A ARG* 4.1 1.3 - - - +
415A PRO* 3.0 21.9 - - - +
429A ARG* 3.6 10.9 - - - +
430A LEU* 3.7 37.9 + - + +
431A SER* 6.0 0.7 - - - -
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Residues in contact with VAL 345 (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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252A LYS* 3.8 34.8 - - + +
256A ARG* 4.2 9.3 + - - +
341A ARG 3.9 11.9 - - - +
342A TYR* 3.5 11.2 - - + +
344A GLU* 1.3 88.3 - - + +
346A ALA* 1.3 66.9 + - - +
347A LYS* 2.9 8.0 + - - +
415A PRO* 4.1 3.0 - - - +
427A ARG* 4.9 1.2 + - - -
429A ARG* 3.8 28.0 + - - +
430A LEU 3.9 21.3 - - - +
431A SER 3.9 9.6 - - - +
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Residues in contact with ALA 346 (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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342A TYR* 2.8 38.9 + - + +
343A ASP* 3.9 13.8 + - - +
344A GLU 3.7 1.4 - - - -
345A VAL* 1.3 74.6 - - - +
347A LYS* 1.3 63.0 + - - +
415A PRO* 3.8 4.3 - - + +
427A ARG* 2.8 20.4 + - - -
505A SO4 3.9 9.4 - - - +
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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