Contacts of the strand formed by residues 59 - 70 (chain G) in PDB entry 4AY9
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 CYS 59 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32G CYS* 3.5 6.1 - - - -
58G THR* 1.3 74.3 + - - +
60G CYS* 1.3 64.7 + - - +
61G VAL* 3.4 6.2 + - + +
84G CYS* 3.1 3.3 - - - -
85G SER* 2.8 32.6 + - - +
87G CYS* 2.0 47.3 - - + -
90G HIS* 4.9 0.4 - - - -
34H THR* 4.0 13.0 - - - +
48H GLN* 3.3 45.1 - - - +
49H LYS 4.6 6.3 - - - -
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Residues in contact with CYS 60 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10G CYS* 2.0 53.2 - - + -
28G CYS* 3.8 2.5 - - - -
29G MET* 3.3 36.6 - - - -
30G GLY 4.1 2.9 - - - +
32G CYS* 3.5 4.8 - - - -
59G CYS* 1.3 72.1 - - - +
61G VAL* 1.3 63.8 + - - +
83G HIS 3.7 0.2 - - - -
34H THR* 3.2 27.2 + - - +
35H ARG 4.1 3.5 - - - +
36H ASP* 3.5 18.9 + - - +
48H GLN* 5.1 0.5 + - - -
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Residues in contact with VAL 61 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28G CYS* 3.8 5.8 - - - -
59G CYS* 4.0 8.1 - - + +
60G CYS* 1.3 81.7 - - - +
62G ALA* 1.3 65.7 + - - +
82G CYS* 3.5 1.2 - - - -
83G HIS* 2.9 60.0 + - + +
85G SER* 3.9 12.8 - - - -
86G THR 4.6 9.4 - - - +
36H ASP* 3.3 18.4 - - + +
48H GLN* 4.1 21.1 - - - +
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Residues in contact with ALA 62 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28G CYS* 3.3 6.1 - - - +
61G VAL* 1.3 76.7 - - - +
63G LYS* 1.3 63.2 + - - +
64G SER 3.9 8.5 - - - +
65G TYR* 4.7 8.1 - - + -
77G GLU* 5.1 0.7 - - - +
79G HIS* 3.2 44.2 - - + +
81G ALA 3.2 10.5 - - - +
83G HIS* 4.3 1.7 - - - -
36H ASP* 3.0 12.3 + - - +
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Residues in contact with LYS 63 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61G VAL 3.3 3.0 + - - -
62G ALA* 1.3 72.8 - - - +
64G SER* 1.3 62.4 + - - +
81G ALA* 2.7 26.0 + - + +
82G CYS 4.3 2.2 - - - +
83G HIS* 3.8 46.5 + - + +
73Z GLU* 4.4 17.6 + - - -
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Residues in contact with SER 64 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62G ALA* 3.3 3.3 - - - +
63G LYS* 1.3 81.7 - - - +
65G TYR* 1.3 72.4 + - - +
79G HIS* 3.9 1.6 - - - -
80G THR* 2.7 37.9 + - - -
81G ALA* 3.4 22.8 + - - +
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Residues in contact with TYR 65 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62G ALA* 4.7 9.6 - - + -
63G LYS 5.7 0.2 - - - -
64G SER* 1.3 85.4 - - - +
66G ASN* 1.3 76.4 + - - +
67G ARG* 2.7 47.4 + - + -
77G GLU* 3.1 41.3 + - + -
78G ASN 3.5 13.9 - - - +
79G HIS* 3.6 15.7 - - + -
80G THR* 3.6 5.3 + - - -
123Z GLN* 5.6 6.7 + - - -
145Z GLN* 4.1 6.9 + - - -
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Residues in contact with ASN 66 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65G TYR* 1.3 83.4 + - - +
67G ARG* 1.3 65.1 + - - +
68G VAL* 4.9 4.9 - - + -
77G GLU* 3.5 0.5 - - - -
78G ASN* 2.8 50.4 + - + +
80G THR* 3.2 22.2 - - - +
1078G NAG 5.7 0.7 + - - -
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Residues in contact with ARG 67 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65G TYR* 2.7 43.9 + - + -
66G ASN* 1.3 73.6 - - - +
68G VAL* 1.3 65.7 + - - +
75G LYS* 5.7 8.5 - - + -
76G VAL 3.7 13.0 - - - +
77G GLU* 4.6 1.6 - - + +
144Z LEU 5.7 2.4 + - - -
145Z GLN* 3.7 20.6 + - - +
171Z GLU* 5.5 7.9 + - - +
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Residues in contact with VAL 68 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25G ILE* 4.4 3.8 - - + -
66G ASN* 3.6 13.2 + - + +
67G ARG* 1.3 80.3 - - - +
69G THR* 1.3 63.7 + - - +
70G VAL* 3.5 15.9 - - + -
74G PHE 3.5 0.3 - - - +
75G LYS* 3.6 5.2 - - - +
76G VAL* 3.0 56.4 + - + +
78G ASN* 4.2 12.6 - - + +
1078G NAG 3.9 27.8 - - + +
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Residues in contact with THR 69 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68G VAL* 1.3 75.3 + - - +
70G VAL* 1.3 68.7 + - - +
72G GLY 5.1 0.9 - - - -
73G GLY* 3.6 34.8 - - - +
74G PHE 3.4 3.6 - - - +
75G LYS* 3.8 19.0 - - + +
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Residues in contact with VAL 70 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18G PHE* 4.1 29.2 - - + +
20G GLN* 6.3 2.0 - - + -
25G ILE* 4.6 3.8 - - + -
68G VAL* 3.5 25.4 - - + -
69G THR* 1.3 80.6 - - - +
71G MET* 1.3 74.9 + - + +
72G GLY* 2.6 20.4 + - - -
73G GLY 3.1 11.6 + - - -
74G PHE* 3.2 18.0 + - + +
76G VAL* 4.1 9.4 - - + -
1078G NAG 4.1 16.2 - - + -
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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