Contacts of the helix formed by residues 63 - 76 (chain B) in PDB entry 4YCG
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 63 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B GLU 3.2 8.7 - - - +
62B PRO* 1.3 89.0 - - + +
64B GLN* 1.3 61.7 + - - +
65B TYR* 3.0 9.4 - - + +
66B MET* 3.1 22.0 + - + +
67B ILE* 3.4 8.8 + - - +
88B SER* 3.3 28.0 - - - +
90B SER* 6.4 1.8 - - - -
230B PHE* 4.5 28.9 - - + -
390D PRO* 4.0 10.5 - - + -
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Residues in contact with GLN 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B PRO 3.6 1.0 + - - -
63B PRO* 1.3 68.9 - - - +
65B TYR* 1.3 55.7 + - - +
66B MET 3.3 0.2 - - - -
67B ILE* 3.6 22.9 - - + -
68B ASP* 2.7 61.9 + - - +
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Residues in contact with TYR 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B PRO* 4.0 2.0 - - + +
64B GLN* 1.3 79.2 - - - +
66B MET* 1.3 58.5 + - + +
68B ASP* 3.4 9.7 + - + +
69B LEU* 2.9 61.3 + - + +
126B GLU* 2.8 27.7 + - - -
128B ARG* 3.8 37.4 + - - +
181B THR* 5.2 0.9 + - - +
230B PHE* 4.3 19.7 - + + -
232B VAL* 3.6 35.7 - - + -
234B PHE* 4.5 4.6 - + - -
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Residues in contact with MET 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B PRO* 5.3 1.3 - - + -
63B PRO* 3.1 16.9 + - + +
65B TYR* 1.3 78.9 - - + +
67B ILE* 1.3 63.0 + - + +
69B LEU* 3.3 11.0 + - - +
70B TYR* 3.1 21.7 + - - +
86B VAL* 3.4 49.1 - - + +
87B ARG 4.3 0.9 - - - +
88B SER* 3.6 29.6 - - - +
230B PHE* 6.2 0.2 - - + -
232B VAL* 4.6 5.4 - - - -
382D LEU* 3.8 16.9 - - + +
390D PRO* 3.5 28.5 - - + +
392D LEU* 3.8 22.4 - - + +
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Residues in contact with ILE 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B PRO* 4.1 20.9 - - + +
63B PRO 3.4 6.0 + - - +
64B GLN* 3.3 27.3 + - + +
66B MET* 1.3 77.6 - - + +
68B ASP* 1.3 59.2 + - - +
70B TYR* 3.2 7.5 + - + +
71B ASN* 3.0 40.5 + - - +
324D ILE* 4.7 9.9 - - + -
382D LEU* 3.8 20.2 - - + -
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Residues in contact with ASP 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B GLN* 2.7 52.8 + - - +
65B TYR* 3.8 10.4 - - + +
67B ILE* 1.3 71.0 - - - +
69B LEU* 1.3 60.0 + - - +
71B ASN* 3.3 15.1 + - - +
72B ARG* 2.8 30.5 + - - +
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Residues in contact with LEU 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B TYR* 2.9 60.7 + - + +
66B MET* 3.5 12.6 - - - +
68B ASP* 1.3 75.2 - - - +
70B TYR* 1.3 59.2 + - - +
72B ARG* 3.6 6.7 - - + +
73B TYR* 2.9 53.9 + - + +
86B VAL* 3.9 28.0 - - + -
234B PHE* 4.4 12.3 - - + -
392D LEU* 3.6 12.3 - - + -
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Residues in contact with TYR 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B MET 3.1 12.3 + - - +
67B ILE* 3.2 10.5 + - + +
69B LEU* 1.3 76.1 - - - +
71B ASN* 1.3 72.0 + - - +
73B TYR* 3.1 3.0 + - - +
74B THR* 2.8 62.5 + - + +
325D ALA* 3.5 30.5 - - + -
326D PRO* 3.2 31.7 - - + +
380D SER* 3.2 26.1 + - - -
382D LEU* 3.9 14.8 - - + -
392D LEU* 3.5 29.5 - - + +
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Residues in contact with ASN 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B ILE* 3.0 33.3 + - - +
68B ASP* 3.7 15.6 + - - +
70B TYR* 1.3 90.8 - - - +
72B ARG* 1.3 52.4 + - - +
74B THR* 3.4 6.4 + - - -
75B THR* 2.5 47.1 + - + +
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Residues in contact with ARG 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B ASP 2.8 18.7 + - - +
69B LEU* 3.6 11.9 - - + +
71B ASN* 1.3 77.2 - - - +
73B TYR* 1.3 74.2 + - + +
75B THR* 3.6 4.7 + - - -
76B ASP* 2.7 67.4 + - - +
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Residues in contact with TYR 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B LEU* 2.9 32.1 + - + +
70B TYR* 3.6 4.7 - - - +
72B ARG* 1.3 86.7 - - + +
74B THR* 1.3 62.0 + - + +
76B ASP 3.4 15.5 - - - +
77B LYS* 3.7 1.9 + - - +
79B SER 5.8 0.7 - - - -
81B PRO* 3.7 40.7 - - + +
83B SER* 4.0 6.8 + - - -
84B ASN 4.8 1.6 - - - -
86B VAL* 3.9 11.8 - - + +
234B PHE* 3.8 24.6 - - - -
380D SER* 4.7 3.8 - - - +
392D LEU* 3.6 34.1 - - + -
394D TYR* 3.3 46.9 - + + -
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Residues in contact with THR 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B TYR* 2.8 61.7 + - + +
71B ASN* 3.3 11.4 + - - -
73B TYR* 1.3 76.6 - - - +
75B THR* 1.3 66.2 + - - +
76B ASP 3.3 0.2 - - - -
77B LYS* 3.2 38.1 - - - +
380D SER* 3.6 19.3 - - - -
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Residues in contact with THR 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B ASN* 2.5 31.2 + - + +
72B ARG* 3.6 6.6 + - - -
74B THR* 1.3 82.2 - - - +
76B ASP* 1.3 72.8 + - - +
77B LYS 3.6 2.0 + - - -
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Residues in contact with ASP 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B ARG* 2.7 55.1 + - - +
73B TYR* 3.4 10.2 - - - +
75B THR* 1.3 88.0 + - - +
77B LYS* 1.3 59.7 + - - +
78B SER* 3.2 8.0 + - - +
79B SER* 3.1 35.3 + - - +
394D TYR* 4.4 0.3 + - - -
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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