Contacts of the helix formed by residues 300 - 311 (chain A) in PDB entry 1ASC
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 ALA 300 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A GLU* 5.0 9.6 - - - +
75A LYS* 6.4 2.0 - - + -
78A LEU* 3.6 30.7 - - + +
83A ILE* 4.1 5.6 - - + +
111A GLN* 4.5 0.7 - - - -
298A PRO 3.5 5.3 + - - -
299A PRO* 1.3 69.6 - - - +
301A HIS* 1.4 59.2 + - - +
303A ALA* 3.1 4.5 + - - +
304A SER* 2.8 33.3 + - - -
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Residues in contact with HIS 301 (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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65A GLU* 2.9 45.0 + - + +
68A LEU* 4.1 19.2 - - + +
72A GLU* 5.4 9.3 + - - -
75A LYS* 5.5 4.4 + - - -
262A LEU* 6.2 0.9 - - + -
265A GLU* 3.8 30.1 - - + +
299A PRO* 3.5 3.8 + - + +
300A ALA* 1.4 75.5 - - - +
302A GLY* 1.3 67.4 + - - +
304A SER* 3.1 5.6 + - - -
305A VAL* 2.9 26.5 + - + +
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Residues in contact with GLY 302 (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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262A LEU* 3.6 6.9 - - - +
265A GLU* 3.8 21.8 + - - +
267A VAL* 3.6 23.1 - - - -
299A PRO* 4.3 3.0 + - - +
300A ALA 3.6 0.4 - - - -
301A HIS* 1.3 81.0 - - - +
303A ALA* 1.3 56.5 + - - +
305A VAL* 3.2 7.6 + - - +
306A VAL* 3.0 29.6 + - - +
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Residues in contact with ALA 303 (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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83A ILE* 4.1 4.0 - - + -
86A PHE* 3.6 21.9 - - + +
111A GLN* 3.4 42.2 - - + +
267A VAL* 3.7 14.2 - - + +
299A PRO 4.2 3.0 + - - +
300A ALA 3.1 5.4 + - - +
302A GLY* 1.3 74.8 - - - +
304A SER* 1.3 60.3 + - - +
306A VAL 3.2 0.4 + - - +
307A ALA* 2.9 30.7 + - - +
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Residues in contact with SER 304 (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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68A LEU* 3.6 25.0 - - - +
72A GLU* 4.4 8.6 + - - +
83A ILE* 3.7 17.8 - - - +
300A ALA* 2.8 22.6 + - - -
301A HIS* 3.4 6.1 - - - -
303A ALA* 1.3 75.9 - - - +
305A VAL* 1.3 62.9 + - - +
307A ALA* 3.6 3.2 + - - +
308A THR* 2.8 30.1 + - - -
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Residues in contact with VAL 305 (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* 3.5 33.4 - - + -
64A ALA* 4.0 5.3 - - + +
65A GLU* 3.5 28.3 - - + +
68A LEU* 3.4 23.6 - - + -
262A LEU* 4.2 12.6 - - + -
301A HIS* 2.9 17.1 + - + +
302A GLY* 3.4 11.0 - - - +
303A ALA 3.2 0.2 - - - -
304A SER* 1.3 77.9 - - - +
306A VAL* 1.3 60.1 + - - +
308A THR* 3.5 1.5 + - - -
309A ILE* 3.3 34.0 + - + +
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Residues in contact with VAL 306 (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 PHE* 4.0 18.2 - - + -
89A CYS* 5.9 0.2 - - + -
256A TYR* 4.1 14.4 - - + -
260A PHE* 3.7 23.3 - - + -
262A LEU* 3.5 20.4 - - + -
267A VAL* 3.8 16.4 - - + -
302A GLY 3.0 16.8 + - - +
303A ALA 3.2 6.0 + - - +
305A VAL* 1.3 73.5 - - - +
307A ALA* 1.3 65.6 + - - +
309A ILE* 3.9 0.5 + - - +
310A LEU* 3.2 44.3 + - + +
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Residues in contact with ALA 307 (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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83A ILE* 4.3 7.9 - - + -
85A GLU* 4.1 12.3 - - + -
86A PHE* 3.9 30.9 - - + +
89A CYS* 4.7 5.1 - - - -
303A ALA 2.9 16.2 + - - +
304A SER* 4.0 4.5 - - - +
306A VAL* 1.3 78.2 - - - +
308A THR* 1.3 51.3 + - - +
310A LEU* 3.9 2.1 - - - +
311A SER* 2.6 40.9 + - - -
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Residues in contact with THR 308 (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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64A ALA* 4.3 21.1 - - + -
67A TYR* 4.1 28.4 - - + -
68A LEU* 3.5 13.6 - - + +
304A SER* 2.8 20.0 + - - -
305A VAL 3.7 4.9 - - - -
306A VAL 3.4 0.2 - - - -
307A ALA* 1.3 70.5 - - - +
309A ILE* 1.3 65.5 + - - +
311A SER* 3.3 12.1 - - - +
312A ASN* 3.1 25.5 - - + +
315A LEU* 4.5 8.1 - - + -
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Residues in contact with ILE 309 (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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60A SER* 3.7 35.4 - - - +
61A VAL* 3.8 16.4 - - + +
64A ALA* 3.8 12.6 - - + -
260A PHE* 3.9 20.9 - - + -
305A VAL* 3.3 24.5 + - + +
306A VAL 4.2 2.7 - - - +
308A THR* 1.3 73.4 - - - +
310A LEU* 1.3 60.9 + - - +
312A ASN 2.8 26.5 - - - +
315A LEU* 3.7 16.8 - - + +
316A ARG* 3.2 10.4 + - - +
319A TRP* 3.5 31.6 - - + -
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Residues in contact with LEU 310 (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 CYS* 3.7 36.2 - - + +
92A GLU* 5.6 0.5 - - - +
93A LEU* 4.7 11.9 - - + -
256A TYR* 4.6 8.5 - - - +
260A PHE* 3.9 10.3 - - + -
306A VAL* 3.2 35.8 + - + +
307A ALA 4.2 0.2 - - - +
309A ILE* 1.3 78.8 - - - +
311A SER* 1.3 56.6 + - - +
312A ASN 3.4 4.1 + - - -
316A ARG* 3.5 45.2 + - - +
319A TRP* 3.4 39.0 - - + -
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Residues in contact with SER 311 (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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85A GLU* 3.6 33.1 + - - -
89A CYS* 4.8 4.9 - - - -
307A ALA 2.6 26.2 + - - -
308A THR* 3.3 6.8 + - - +
310A LEU* 1.3 74.2 - - - +
312A ASN* 1.3 61.5 + - - +
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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