Contacts of the helix formed by residues 339 - 354 (chain A) in PDB entry 2A1H
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 339 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A VAL* 4.3 16.4 - - + -
307A GLU* 3.5 14.6 - - - +
319A PRO* 5.0 0.7 - - + -
334A THR* 3.4 21.8 - - + +
335A MET* 4.0 33.2 - - + -
337A ASN 3.6 1.3 - - - +
338A GLY* 1.4 76.4 - - - +
340A GLU* 1.3 59.8 + - - +
341A LEU 3.5 2.2 - - - -
342A ILE* 3.3 24.5 + - + -
343A LEU* 2.9 40.7 + - + +
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Residues in contact with GLU 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A TYR* 5.3 1.4 + - - -
306A ARG* 3.1 26.6 + - - +
307A GLU* 3.5 4.1 + - - +
337A ASN 3.1 18.0 + - - +
338A GLY* 3.4 4.7 - - - -
339A PRO* 1.3 70.9 - - - +
341A LEU* 1.3 57.7 + - - +
343A LEU* 3.5 7.0 + - - +
344A ARG* 3.1 30.2 + - + +
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Residues in contact with LEU 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A TYR* 3.6 42.8 - - + +
256A LEU* 3.9 20.0 - - + -
281A TRP* 3.5 32.5 - - + -
284A PHE* 3.7 15.9 - - + -
307A GLU* 2.9 22.2 + - - +
309A PHE* 4.2 5.2 - - + -
340A GLU* 1.3 70.6 - - - +
342A ILE* 1.3 60.3 + - - +
344A ARG* 3.2 8.0 + - + +
345A PHE* 2.9 47.8 + - + +
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Residues in contact with ILE 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A VAL* 4.4 6.1 - - + -
307A GLU* 3.0 20.8 + - - +
309A PHE* 3.7 42.4 - - + -
317A VAL* 3.9 15.7 - - + +
319A PRO* 3.8 11.9 - - + -
334A THR* 3.6 27.6 - - + -
339A PRO* 3.3 15.7 + - + +
341A LEU* 1.3 75.0 - - - +
343A LEU* 1.3 57.3 + - - +
345A PHE* 3.3 8.4 + - - +
346A GLN* 2.9 52.7 + - - +
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Residues in contact with LEU 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A VAL* 4.2 16.6 - - + -
338A GLY* 4.2 8.5 - - - +
339A PRO* 2.9 38.3 + - + +
340A GLU* 3.8 6.5 - - - +
342A ILE* 1.3 75.1 - - - +
344A ARG* 1.3 56.6 + - - +
346A GLN* 3.6 19.5 - - + +
347A LYS* 3.1 30.1 + - - +
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Residues in contact with ARG 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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281A TRP* 3.5 49.7 - - + +
283A GLU* 2.7 42.6 + - - -
284A PHE* 5.2 3.2 - - - -
340A GLU* 3.1 19.5 + - + +
341A LEU* 3.2 9.2 + - - +
343A LEU* 1.3 74.0 - - - +
345A PHE* 1.3 64.0 + - - +
347A LYS* 3.5 9.0 + - + +
348A GLU* 3.1 46.9 + - + +
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Residues in contact with PHE 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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256A LEU* 3.9 16.6 - - + -
274A LEU* 3.5 49.8 - - + -
277A MET* 3.6 26.4 - - + +
278A ALA* 3.9 5.8 - - + -
281A TRP* 3.5 20.4 - + - -
309A PHE* 3.7 34.1 - + - -
317A VAL* 4.2 12.3 - - + -
341A LEU* 2.9 38.3 + - + +
342A ILE* 3.6 4.7 - - - +
344A ARG* 1.3 76.3 - - - +
346A GLN* 1.3 56.7 + - - +
348A GLU* 3.9 0.9 - - - +
349A LEU* 2.9 37.1 + - - +
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Residues in contact with GLN 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A PHE* 4.0 8.5 - - - -
179A VAL* 3.2 31.4 - - - +
315A CYS 5.1 0.8 + - - -
316A GLN* 5.6 1.3 - - + +
317A VAL* 3.2 43.9 + - + +
342A ILE* 2.9 16.5 + - - +
343A LEU* 3.6 23.5 - - + +
344A ARG 3.3 0.2 - - - -
345A PHE* 1.3 76.7 - - - +
347A LYS* 1.3 56.0 + - - +
349A LEU* 3.9 2.4 - - - +
350A LYS* 3.1 64.1 + - - +
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Residues in contact with LYS 347 (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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343A LEU 3.1 18.1 + - - +
344A ARG* 3.8 8.7 - - + +
346A GLN* 1.3 76.3 - - - +
348A GLU* 1.3 62.4 + - + +
350A LYS* 3.4 7.9 + - - +
351A GLU* 3.1 56.5 + - + +
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Residues in contact with GLU 348 (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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277A MET* 3.8 22.9 - - + +
281A TRP* 3.0 32.3 + - - -
344A ARG* 3.1 45.8 + - + +
347A LYS* 1.3 80.0 - - + +
349A LEU* 1.3 62.8 + - - +
351A GLU* 3.6 11.3 + - - +
352A ILE* 3.4 29.1 + - - +
357A ARG* 3.6 21.3 + - - +
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Residues in contact with LEU 349 (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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91A PHE* 3.9 31.6 - - + -
270A VAL* 4.5 8.7 - - + -
273A SER* 4.8 5.6 - - - -
274A LEU* 3.9 22.9 - - + -
277A MET* 4.1 19.1 - - + -
316A GLN* 3.6 24.9 - - + +
317A VAL* 5.1 3.4 - - + -
345A PHE* 2.9 24.6 + - + +
346A GLN* 3.9 5.6 - - - +
348A GLU* 1.3 76.0 - - - +
350A LYS* 1.3 55.1 + - - +
352A ILE* 3.3 5.1 + - + +
353A GLN* 2.8 54.3 + - - +
361A TRP* 4.6 3.6 - - + -
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Residues in contact with LYS 350 (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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137A GLY* 5.6 9.4 - - - +
316A GLN* 4.8 17.0 - - - +
346A GLN* 3.1 53.8 + - + +
347A LYS* 3.8 6.7 - - - +
349A LEU* 1.3 80.0 - - - +
351A GLU* 1.3 55.7 + - + +
353A GLN* 4.3 5.2 + - - +
354A TYR* 3.0 60.9 + - + +
356A ILE* 4.7 1.3 - - - +
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Residues in contact with GLU 351 (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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347A LYS* 3.1 43.6 + - + +
348A GLU* 3.8 15.2 - - - +
349A LEU 3.3 0.4 - - - -
350A LYS* 1.3 76.8 - - + +
352A ILE* 1.3 60.2 + - - +
355A GLY 3.7 0.3 + - - -
356A ILE* 3.0 49.7 + - + +
357A ARG* 3.1 42.2 + - + +
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Residues in contact with ILE 352 (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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91A PHE* 4.6 3.8 - - + -
277A MET* 4.0 20.6 - - + -
348A GLU 3.4 15.9 + - - +
349A LEU* 3.3 7.8 + - - +
351A GLU* 1.3 76.2 - - - +
353A GLN* 1.3 64.2 + - - +
355A GLY* 3.5 8.7 + - - -
357A ARG* 3.9 41.2 - - - +
359A HIS* 3.8 38.1 - - + +
361A TRP* 4.0 23.3 - - + -
362A MET* 3.3 34.8 - - + +
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Residues in contact with GLN 353 (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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81A PHE* 3.3 58.6 - - + +
89A ARG* 4.6 4.5 + - - -
91A PHE* 3.7 45.5 - - + -
316A GLN* 3.0 32.8 + - - +
349A LEU* 2.8 33.0 + - - +
350A LYS* 4.2 10.2 + - - +
352A ILE* 1.3 76.6 - - + +
354A TYR* 1.3 62.1 + - + +
355A GLY 3.3 2.9 + - - -
362A MET* 3.6 14.6 - - - +
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Residues in contact with TYR 354 (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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81A PHE* 3.7 29.9 - + + -
82A LYS 3.4 26.2 - - - -
83A GLY* 3.4 22.6 - - - +
84A LYS* 4.5 1.8 + - + -
85A ASP* 5.4 1.2 - - - +
89A ARG* 4.0 5.5 + - - -
133A PRO 5.7 0.9 - - - -
134A ASP 5.2 2.7 - - - -
135A ALA 4.5 9.4 - - - -
136A ALA* 5.6 0.7 - - - -
137A GLY* 3.4 16.3 - - - -
138A THR 2.7 39.7 + - - -
350A LYS* 3.0 51.2 + - + +
353A GLN* 1.3 77.8 - - + +
355A GLY* 1.3 61.1 + - - +
356A ILE* 3.5 17.4 + - + +
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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
------------------------------------------------------------
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