Contacts of the helix formed by residues 311 - 322 (chain A) in PDB entry 1IAY
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 SER 311 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285A PHE 5.4 1.2 + - - -
309A LEU 3.6 3.1 + - - -
310A VAL* 1.3 76.6 - - - +
312A THR* 1.3 55.4 + - - +
313A GLN* 3.5 18.0 + - - +
314A THR* 2.7 22.6 + - - -
315A GLN* 2.7 31.0 + - - +
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Residues in contact with THR 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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86A ILE* 2.6 38.1 + - - +
87A ALA* 4.4 4.5 + - - -
89A PHE* 3.3 35.2 - - + +
95A LEU* 4.3 6.5 - - + +
310A VAL 3.3 2.7 + - - +
311A SER* 1.3 73.2 + - - +
313A GLN* 1.3 60.3 + - - +
315A GLN* 3.6 23.4 - - - +
316A TYR* 2.9 31.5 + - - +
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Residues in contact with GLN 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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74A SER* 5.7 4.6 - - - -
75A ILE* 5.3 21.0 + - + +
83A PHE* 5.8 5.3 - - - -
86A ILE* 4.4 16.8 - - + -
311A SER* 3.0 12.1 + - - +
312A THR* 1.3 86.1 + - - +
314A THR* 1.3 64.2 + - - +
316A TYR* 3.7 4.2 - - - +
317A PHE* 3.5 17.8 + - - +
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Residues in contact with THR 314 (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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285A PHE* 4.0 40.0 + - + +
287A VAL* 4.1 0.9 - - + -
310A VAL* 3.8 18.2 - - + -
311A SER* 2.7 25.8 + - - -
313A GLN* 1.3 77.7 + - - +
315A GLN* 1.3 63.4 + - - -
316A TYR 3.1 1.8 - - - -
317A PHE* 3.4 6.3 + - + +
318A LEU* 3.1 40.0 + - + +
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Residues in contact with GLN 315 (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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89A PHE* 5.3 1.2 - - - -
91A ASP 5.6 0.6 + - - -
94A GLY* 3.3 9.2 - - - -
95A LEU* 2.8 38.9 + - + +
98A PHE* 3.4 35.3 - - + +
123A MET* 3.9 18.5 - - - +
309A LEU* 5.6 0.8 - - - +
310A VAL* 3.1 33.1 + - + -
311A SER 2.7 17.1 + - - +
312A THR* 3.2 26.2 + - - +
314A THR* 1.3 72.7 - - - +
316A TYR* 1.3 58.4 + - - +
318A LEU 3.5 0.2 + - - -
319A ALA* 3.0 31.0 + - - +
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Residues in contact with TYR 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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72A LYS 3.8 8.8 + - - -
73A GLY* 3.6 15.9 - - - -
74A SER* 3.5 31.2 - - - -
75A ILE 4.8 0.9 - - - -
76A CYS* 5.0 1.8 - - - -
77A SER* 3.6 23.1 + - - -
82A SER* 3.7 23.7 + - - -
86A ILE* 3.5 31.0 - - + -
95A LEU* 3.8 12.1 - - + +
312A THR 2.9 16.2 + - - +
313A GLN 3.7 6.5 - - - +
315A GLN* 1.3 78.1 - - - +
317A PHE* 1.3 61.7 + - - +
319A ALA* 3.2 7.1 + - + +
320A ALA* 3.1 22.2 + - + +
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Residues in contact with PHE 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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63A ILE* 4.6 4.9 - - + -
66A TRP* 3.7 21.5 - + - -
67A ILE* 3.8 35.2 - - + -
73A GLY 3.1 29.8 - - - +
74A SER* 4.9 7.9 - - - -
282A LEU* 5.3 1.6 - - + -
285A PHE* 4.0 25.6 - + - -
313A GLN 3.5 10.6 + - - +
314A THR* 3.4 9.7 + - - +
316A TYR* 1.3 80.0 - - - +
318A LEU* 1.3 80.5 + - + +
320A ALA* 3.4 2.4 + - - +
321A MET* 3.1 43.4 + - + +
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Residues in contact with LEU 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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98A PHE* 4.5 15.5 - - + -
101A ALA* 4.9 0.7 - - - -
276A LEU* 3.5 28.3 - - + -
280A MET* 5.5 0.4 - - - -
282A LEU* 4.2 18.4 - - + -
285A PHE* 4.9 2.7 - - + -
287A VAL* 3.5 25.1 - - + -
314A THR* 3.1 24.5 + - + +
315A GLN 4.1 2.2 - - - +
317A PHE* 1.3 96.1 - - + +
319A ALA* 1.3 61.7 + - - +
320A ALA 3.0 1.6 - - - -
321A MET* 4.4 12.3 - - + +
322A LEU* 2.8 47.5 + - + +
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Residues in contact with ALA 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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95A LEU* 5.4 3.4 - - + -
97A GLU* 3.8 28.5 - - + +
98A PHE* 3.9 10.0 - - + +
101A ALA* 4.0 11.6 - - - +
315A GLN 3.0 20.5 + - - +
316A TYR* 3.2 7.2 + - - +
318A LEU* 1.3 76.3 - - - +
320A ALA* 1.3 56.8 + - - +
323A SER* 2.4 34.8 + - - -
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Residues in contact with ALA 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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66A TRP* 3.8 13.3 - - + -
72A LYS 5.2 0.7 - - - +
73A GLY* 3.9 25.6 - - - -
316A TYR* 3.1 14.6 + - + +
317A PHE 3.5 9.4 - - - +
319A ALA* 1.3 76.0 - - - +
321A MET* 1.3 65.5 + - - +
323A SER* 3.3 15.6 + - - -
324A ASP* 3.6 5.9 + - - +
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Residues in contact with MET 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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63A ILE* 4.0 20.4 - - + -
66A TRP* 3.4 34.9 - - + -
280A MET* 3.3 38.6 - - + -
282A LEU* 5.1 1.3 - - + -
317A PHE* 3.1 34.8 + - + +
318A LEU* 4.4 13.9 - - + +
320A ALA* 1.3 79.2 - - - +
322A LEU* 1.3 66.7 + - + +
323A SER 3.1 0.4 - - - -
324A ASP* 3.3 17.7 + - - +
327A PHE* 3.5 36.3 - - + -
328A VAL* 3.8 1.4 - - - +
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Residues in contact with LEU 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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101A ALA* 3.7 35.4 - - + +
102A ILE* 4.0 23.3 - - + -
104A LYS* 5.6 3.3 - - - +
105A PHE* 3.7 39.6 + - + +
276A LEU* 4.6 11.9 - - + -
280A MET* 4.0 24.0 - - + -
318A LEU* 2.8 33.0 + - + +
321A MET* 1.3 76.1 - - + +
323A SER* 1.3 61.4 + - - +
324A ASP 3.3 0.4 - - - -
325A GLU* 5.1 0.5 + - - -
328A VAL* 3.8 18.6 - - + +
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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