Contacts of the helix formed by residues 63 - 76 (chain A) in PDB entry 4Y2H
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 63 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59A GLU 3.0 14.6 + - - +
60A MET 3.2 12.6 - - - +
61A ILE 3.0 2.7 - - - -
62A ALA* 1.3 72.9 - - - +
64A ARG* 1.3 59.4 + - - +
65A VAL* 3.3 9.2 + - - +
66A ARG* 3.1 26.4 + - + +
67A THR* 3.0 31.2 + - - -
315A ALA 4.5 1.4 - - - +
316A THR* 3.5 12.3 - - - -
317A HIS* 2.7 47.5 + - + +
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Residues in contact with ARG 64 (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 2.9 9.3 + - - +
63A ASP* 1.3 70.8 + - - +
65A VAL* 1.3 92.1 + - - +
68A ASP* 2.9 54.5 + - - +
314A PRO* 4.6 12.5 - - - +
215B TYR* 3.5 15.7 - - + +
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Residues in contact with VAL 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ASP* 3.3 6.3 + - - +
64A ARG* 1.3 103.1 - - - +
66A ARG* 1.3 64.0 + - - +
68A ASP* 4.0 1.0 - - - +
69A ALA* 3.1 27.3 + - + +
307A LEU* 3.7 19.5 - - + -
308A SER 4.6 6.1 - - - +
314A PRO* 3.9 25.8 - - + +
315A ALA 4.0 11.7 - - - +
316A THR* 4.0 13.5 - - + -
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Residues in contact with ARG 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A MET* 2.8 39.5 + - - +
61A ILE* 4.1 6.1 - - - +
63A ASP* 3.1 23.4 + - - +
65A VAL* 1.3 78.5 - - - +
67A THR* 1.3 78.7 + - - +
69A ALA* 3.4 2.6 + - - +
70A TYR* 3.3 31.6 + - + -
95A ILE* 4.8 2.2 - - - +
96A LEU* 5.1 4.0 - - - +
155A GLU* 2.8 37.8 + - + +
307A LEU* 4.1 12.8 - - + +
316A THR* 5.1 0.2 - - - +
317A HIS* 3.7 16.2 - - - -
318A TRP* 3.5 34.5 - - + -
401A SAH 2.6 43.4 + - - -
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Residues in contact with THR 67 (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 MET 3.1 22.7 + - - -
61A ILE* 3.5 5.9 + - + -
63A ASP 3.0 10.2 + - - -
66A ARG* 1.3 91.1 + - - +
68A ASP* 1.3 58.6 + - - +
70A TYR* 3.6 5.7 + - - +
71A ARG* 2.9 26.3 + - - +
95A ILE* 4.1 11.9 - - + -
96A LEU* 5.4 1.6 - - + -
99A PHE* 4.0 19.2 - - + -
215B TYR* 3.6 37.2 - - + -
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Residues in contact with ASP 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ARG* 2.9 45.4 + - + +
65A VAL* 4.5 1.1 - - - +
67A THR* 1.3 74.5 - - - +
69A ALA* 1.3 60.2 + - - +
71A ARG* 2.3 44.1 + - - +
72A LEU* 3.0 38.6 + - + +
214B HIS 4.9 1.6 - - - +
215B TYR* 3.6 14.9 - - - -
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Residues in contact with ALA 69 (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 VAL* 3.1 21.2 + - + +
66A ARG 3.6 4.5 - - - +
67A THR 3.3 0.2 - - - -
68A ASP* 1.3 73.8 - - - +
70A TYR* 1.3 56.5 + - - +
73A GLY* 2.7 35.9 + - - -
296A PHE* 4.3 4.3 - - + -
305A LEU* 3.6 31.0 - - + +
307A LEU* 4.1 24.2 - - + -
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Residues in contact with TYR 70 (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 ARG* 3.3 21.3 + - + +
67A THR* 3.9 5.8 - - - +
69A ALA* 1.3 78.8 - - - +
71A ARG* 1.3 53.4 + - - +
74A ILE* 2.8 43.1 + - + +
96A LEU* 3.6 34.3 - - + -
153A VAL* 4.1 15.9 - - + -
154A SER 2.7 34.1 + - - -
155A GLU* 3.1 32.4 - - + -
157A MET* 3.4 10.8 - - + +
186A PRO* 3.4 12.7 - - + +
296A PHE* 3.7 35.4 - + - -
307A LEU* 4.0 16.6 - - + -
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Residues in contact with ARG 71 (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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67A THR 2.9 19.2 + - - +
68A ASP* 2.3 38.1 + - - +
69A ALA 3.3 0.2 - - - -
70A TYR* 1.3 76.3 - - - +
72A LEU* 1.3 90.4 + - - +
74A ILE* 3.9 1.6 - - - +
75A LEU* 3.1 50.8 + - + +
99A PHE* 3.3 37.7 - - + +
102A GLN* 5.9 0.4 - - - -
214B HIS 4.2 9.8 + - - -
215B TYR* 3.9 27.6 + - + +
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Residues in contact with LEU 72 (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 ASP* 3.0 25.9 + - + +
71A ARG* 1.3 105.9 - - - +
73A GLY* 1.3 66.7 + - - +
75A LEU* 3.2 10.4 + - + +
76A ARG* 2.9 43.8 + - - +
305A LEU* 3.6 19.3 - - + -
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Residues in contact with GLY 73 (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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69A ALA 2.7 22.7 + - - -
70A TYR 3.8 0.4 - - - -
72A LEU* 1.3 73.2 - - - +
74A ILE* 1.3 58.5 + - - +
76A ARG* 3.8 7.7 - - - +
77A ASN* 2.9 30.3 + - - -
185A LEU* 4.0 5.5 - - - +
296A PHE* 4.1 25.4 - - - -
305A LEU* 4.0 5.6 - - - +
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Residues in contact with ILE 74 (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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70A TYR* 2.8 33.4 + - + +
71A ARG 3.9 2.2 - - - +
73A GLY* 1.3 72.9 - - - +
75A LEU* 1.3 65.8 + - + +
77A ASN* 3.1 12.3 + - - -
78A TRP 3.9 0.3 + - - -
81A LEU* 3.6 16.1 - - + +
96A LEU* 4.0 14.4 - - + +
99A PHE* 3.6 52.5 - - + +
100A CYS* 3.8 16.4 - - - +
103A ALA* 4.0 7.5 - - + +
153A VAL* 4.1 20.0 - - + -
185A LEU* 3.9 21.3 - - + -
296A PHE* 5.6 0.2 - - + -
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Residues in contact with LEU 75 (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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71A ARG* 3.1 45.0 + - + +
72A LEU* 3.2 8.5 + - + +
74A ILE* 1.3 78.9 - - + +
76A ARG* 1.3 58.6 + - - +
77A ASN 3.1 0.9 + - - -
78A TRP* 3.1 29.1 + - - +
99A PHE* 4.0 13.9 - - + +
102A GLN* 4.6 10.1 - - + +
103A ALA* 3.8 29.6 - - + +
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Residues in contact with ARG 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A LEU* 2.9 33.8 + - - +
73A GLY* 3.8 14.4 - - - +
75A LEU* 1.3 75.5 - - - +
77A ASN* 1.3 62.0 + - - +
78A TRP* 3.3 14.2 + - - -
79A ALA 5.1 0.3 + - - -
296A PHE* 6.1 0.2 - - - -
297A PRO 4.4 2.7 - - - +
298A GLY* 4.3 7.4 - - - -
299A GLY* 3.2 24.6 - - - +
300A GLU* 4.1 2.8 + - - +
301A SER* 4.4 18.3 + - - +
303A LYS* 2.8 43.5 + - - +
304A PRO 4.3 1.4 + - - -
305A LEU* 4.0 33.1 - - - +
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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