Contacts of the helix formed by residues 317 - 329 (chain A) in PDB entry 4H1S
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 ASP 317 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62A ALA* 2.9 20.9 + - - +
65A PHE* 3.4 38.0 - - + -
66A THR* 3.2 9.0 + - - +
69A GLN* 4.6 7.1 + - - -
316A GLU* 1.3 70.0 - - - +
318A PRO* 1.3 70.2 - - - +
319A SER* 3.2 12.9 + - - -
320A ILE* 2.9 34.2 + - + +
321A LYS* 2.8 30.7 + - - +
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Residues in contact with PRO 318 (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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316A GLU 3.4 8.3 - - - +
317A ASP* 1.3 92.9 - - - +
319A SER* 1.3 58.2 - - - +
321A LYS* 3.4 8.3 + - + +
322A ALA* 2.9 31.0 + - - +
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Residues in contact with SER 319 (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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317A ASP* 3.2 10.4 + - - -
318A PRO* 1.3 75.1 - - - +
320A ILE* 1.3 70.3 + - - +
322A ALA* 3.3 6.4 + - - +
323A ASP* 3.1 22.2 + - - +
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Residues in contact with ILE 320 (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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61A VAL* 4.0 18.8 - - + -
62A ALA* 3.6 31.2 - - + +
65A PHE* 3.7 37.5 - - + -
104A PHE* 4.1 11.4 - - + -
107A ALA* 4.0 24.7 - - + +
108A LEU* 4.5 3.1 - - + -
317A ASP* 2.9 22.0 + - - +
319A SER* 1.3 76.5 - - - +
321A LYS* 1.3 56.9 + - - +
323A ASP* 3.0 10.7 + - - +
324A ILE* 2.8 27.7 + - + +
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Residues in contact with LYS 321 (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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62A ALA* 3.8 13.4 - - + +
316A GLU* 3.8 35.6 + - + +
317A ASP 2.8 23.3 + - - +
318A PRO* 3.7 7.6 - - + +
320A ILE* 1.3 72.0 - - - +
322A ALA* 1.3 56.7 - - - +
324A ILE* 3.2 9.2 + - + +
325A ASN* 2.8 47.9 + - - +
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Residues in contact with ALA 322 (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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318A PRO 2.9 18.7 + - - +
319A SER* 3.7 6.7 - - - +
321A LYS* 1.3 76.3 - - - +
323A ASP* 1.3 58.5 + - - +
325A ASN* 3.4 9.3 + - - +
326A LYS* 2.9 27.9 + - - +
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Residues in contact with ASP 323 (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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103A HIS* 2.5 35.4 + - - -
104A PHE* 3.8 9.7 - - + -
107A ALA* 5.6 2.6 - - - +
319A SER 3.1 12.9 + - - +
320A ILE* 3.0 13.0 + - + +
322A ALA* 1.3 74.7 - - - +
324A ILE* 1.3 63.5 + - - +
326A LYS* 3.2 16.6 + - - +
327A TRP* 2.9 52.1 + - - -
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Residues in contact with ILE 324 (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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41A LEU* 4.2 13.2 - - + +
42A GLU* 4.2 19.1 - - + +
61A VAL* 3.6 30.1 - - + -
62A ALA* 5.1 3.1 - - + -
92A TRP* 3.5 24.9 - - + -
104A PHE* 3.4 27.1 - - + -
320A ILE* 2.8 21.1 + - + +
321A LYS* 3.4 14.6 - - + +
323A ASP* 1.3 73.4 - - - +
325A ASN* 1.3 64.4 + - - +
327A TRP 3.2 1.7 + - - -
328A ARG* 2.8 31.5 + - + +
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Residues in contact with ASN 325 (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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321A LYS* 2.8 44.6 + - - +
322A ALA* 3.7 8.7 - - - +
324A ILE* 1.3 78.8 - - - +
326A LYS* 1.3 63.0 + - - +
328A ARG* 3.3 17.6 + - - +
329A ILE* 3.6 16.6 + - - +
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Residues in contact with LYS 326 (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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322A ALA 2.9 14.5 + - - +
323A ASP* 3.3 24.7 + - - +
324A ILE 3.2 0.2 - - - -
325A ASN* 1.3 78.8 - - - +
327A TRP* 1.3 68.5 + - + +
328A ARG 3.4 0.5 + - - -
329A ILE* 3.5 17.8 + - - +
330A LYS 4.8 0.5 + - - -
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Residues in contact with TRP 327 (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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92A TRP* 3.4 25.6 - + + -
96A TYR* 2.5 69.6 + + - -
99A ALA* 4.1 11.4 - - + -
100A GLU* 3.8 21.1 - - + -
103A HIS* 3.5 46.8 + + + -
104A PHE* 4.3 5.8 - + - -
323A ASP* 2.9 47.0 + - - +
326A LYS* 1.3 86.3 - - + +
328A ARG* 1.3 61.6 + - - +
329A ILE 3.2 1.9 + - - -
330A LYS 3.8 3.2 + - - -
331A LEU* 4.0 3.3 - - - +
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Residues in contact with ARG 328 (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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42A GLU* 2.8 42.7 + - - +
50A LYS* 3.5 11.9 - - - +
91A ILE* 4.2 6.3 - - - +
92A TRP* 4.2 12.0 - - + +
324A ILE* 2.8 19.7 + - + +
325A ASN* 3.6 15.9 - - - +
326A LYS 3.2 1.0 - - - -
327A TRP* 1.3 76.8 - - - +
329A ILE* 1.3 65.5 + - + +
330A LYS 3.4 0.2 - - - -
331A LEU* 3.1 28.7 + - - +
332A ASP* 2.8 44.3 + - - +
334A TYR 5.8 0.8 - - - -
409A GLU* 2.9 43.2 + - - -
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Residues in contact with ILE 329 (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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325A ASN 3.6 15.0 + - - +
326A LYS* 3.7 12.3 - - - +
327A TRP 3.2 0.8 - - - -
328A ARG* 1.3 77.6 - - + +
330A LYS* 1.3 65.4 + - - +
331A LEU 3.0 1.7 + - - -
332A ASP* 3.2 30.5 + - - +
333A ASN 4.7 0.9 + - - -
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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