Contacts of the helix formed by residues 72 - 90 (chain d) in PDB entry 6QY3
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 THR 72 (chain d).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69d ASP 5.5 2.5 - - - -
70d ILE 3.6 5.6 + - - -
71d ASN* 1.3 74.4 - - - +
73d SER* 1.3 61.8 + - - +
74d GLN* 3.3 6.7 - - - -
75d VAL* 3.8 13.3 - - - +
76d LEU* 2.8 31.4 + - - +
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Residues in contact with SER 73 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551 T 5.9 3.1 - - - -
72d THR* 1.3 73.8 - - - +
74d GLN* 1.3 57.6 + - - +
76d LEU* 3.9 3.3 - - - +
77d LYS* 2.9 31.4 + - - +
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Residues in contact with GLN 74 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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541 T 5.3 10.1 - - - +
72d THR* 3.3 4.1 - - - -
73d SER* 1.3 77.0 - - - +
75d VAL* 1.3 61.0 + - - +
77d LYS* 3.8 4.0 - - - +
78d LEU* 2.9 32.4 + - - +
157d TYR 5.5 1.3 - - - +
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Residues in contact with VAL 75 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70d ILE 4.1 19.5 - - - +
71d ASN* 5.3 0.4 - - - -
72d THR* 3.4 16.7 + - - +
73d SER 3.4 0.4 - - - -
74d GLN* 1.3 78.7 - - - +
76d LEU* 1.3 55.9 + - - +
78d LEU* 3.9 3.3 - - - +
79d LEU* 2.9 30.9 + - - +
154d ILE* 5.5 8.3 - - + +
157d TYR* 5.0 17.1 - - + +
158d LEU 6.2 0.4 - - - +
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Residues in contact with LEU 76 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71d ASN* 5.9 3.1 - - + +
72d THR 2.8 19.5 + - - +
73d SER* 4.2 3.1 - - - +
75d VAL* 1.3 74.6 - - - +
77d LYS* 1.3 59.9 + - - +
79d LEU* 3.7 5.5 - - - +
80d HIS* 2.9 29.6 + - - +
135d VAL 4.9 13.3 - - - +
136d ARG* 5.8 5.4 - - + -
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Residues in contact with LYS 77 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73d SER 2.9 20.6 + - - +
74d GLN* 3.8 4.9 - - - +
76d LEU* 1.3 77.6 - - - +
78d LEU* 1.3 57.1 + - - +
80d HIS* 3.2 7.3 + - - +
81d THR* 2.9 27.8 + - - -
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Residues in contact with LEU 78 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74d GLN 2.9 17.4 + - - +
75d VAL 4.2 2.5 - - - +
77d LYS* 1.3 76.4 - - - +
79d LEU* 1.3 58.6 + - - +
81d THR* 3.4 8.7 + - - -
82d ASP* 2.9 27.5 + - - +
157d TYR* 4.6 23.3 - - + +
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Residues in contact with LEU 79 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75d VAL 2.9 20.7 + - - +
76d LEU* 3.7 7.4 - - - +
78d LEU* 1.3 75.2 - - - +
80d HIS* 1.3 59.1 + - - +
82d ASP* 3.1 8.6 + - - +
83d ILE* 2.9 27.7 + - - +
157d TYR* 5.7 3.0 - - + +
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Residues in contact with HIS 80 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76d LEU 2.9 18.4 + - - +
77d LYS* 3.6 6.5 - - - +
79d LEU* 1.3 75.7 - - - +
81d THR* 1.3 57.7 + - - +
83d ILE* 3.3 7.4 + - - +
84d VAL* 2.9 28.1 + - - +
127d LEU* 5.7 9.1 - - + +
130d ILE* 4.8 20.7 - - + +
131d LYS* 5.9 2.0 - - + +
135d VAL* 6.4 2.9 - - + -
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Residues in contact with THR 81 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77d LYS 2.9 13.3 + - - -
78d LEU* 3.6 12.3 - - - -
79d LEU 3.2 0.4 - - - -
80d HIS* 1.3 77.9 - - - +
82d ASP* 1.3 56.2 + - - +
84d VAL* 3.3 7.9 + - - +
85d SER* 2.9 28.1 + - - -
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Residues in contact with ASP 82 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78d LEU 2.9 14.7 + - - +
79d LEU* 3.1 11.4 + - - +
81d THR* 1.3 76.9 - - - +
83d ILE* 1.3 57.6 + - - +
85d SER* 3.2 8.0 + - - -
86d GLN* 2.9 27.2 + - - +
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Residues in contact with ILE 83 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111a GLU* 5.8 6.3 - - + +
79d LEU 2.9 15.8 + - - +
80d HIS* 3.7 7.6 - - - +
82d ASP* 1.3 76.0 - - - +
84d VAL* 1.3 58.0 + - - +
86d GLN* 3.2 8.4 + - - +
87d LEU* 2.9 29.1 + - - +
130d ILE* 5.9 5.8 - - + -
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Residues in contact with VAL 84 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80d HIS 2.9 17.4 + - - +
81d THR* 3.6 8.7 - - - +
83d ILE* 1.3 76.3 - - - +
85d SER* 1.3 57.4 + - - +
87d LEU* 3.5 7.3 + - - +
88d ASN* 2.9 28.6 + - - +
126d LEU* 5.4 13.7 - - + -
127d LEU* 5.5 11.4 - - + +
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Residues in contact with SER 85 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81d THR 2.9 14.0 + - - -
82d ASP* 3.5 11.2 - - - -
83d ILE 3.2 0.2 - - - -
84d VAL* 1.3 74.7 - - - +
86d GLN* 1.3 59.4 + - - +
88d ASN* 3.1 7.7 + - - +
89d ASP* 2.9 28.4 + - - +
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Residues in contact with GLN 86 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111a GLU* 5.7 10.5 - - + +
82d ASP 2.9 14.0 + - - +
83d ILE* 3.6 11.0 - - - +
85d SER* 1.3 77.1 - - - +
87d LEU* 1.3 61.9 + - - +
89d ASP* 3.4 17.2 + - - +
90d LYS* 4.0 6.9 + - - +
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Residues in contact with LEU 87 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111a GLU* 5.8 8.4 - - + +
83d ILE 2.9 16.0 + - - +
84d VAL* 3.8 7.2 - - - +
86d GLN* 1.3 76.3 - - - +
88d ASN* 1.3 59.9 + - - +
89d ASP 3.3 0.2 - - - -
90d LYS* 3.3 20.2 + - - +
93d VAL* 5.0 6.3 - - + +
94d ARG* 3.8 14.6 + - + +
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Residues in contact with ASN 88 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84d VAL 2.9 18.6 + - - +
85d SER* 3.1 9.2 + - - +
87d LEU* 1.3 74.1 - - - +
89d ASP* 1.3 63.9 + - - +
90d LYS 3.2 6.5 + - - +
91d PRO* 4.7 1.6 - - - +
94d ARG* 5.0 6.9 - - - +
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Residues in contact with ASP 89 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85d SER 2.9 15.4 + - - +
86d GLN* 3.7 10.8 - - - +
87d LEU 3.3 0.8 - - - -
88d ASN* 1.3 77.1 - - - +
90d LYS* 1.3 58.9 + - - +
91d PRO 3.9 1.6 - - - -
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Residues in contact with LYS 90 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86d GLN 4.0 6.3 + - - +
87d LEU* 3.3 17.5 + - - +
88d ASN 3.2 2.5 - - - +
89d ASP* 1.3 77.2 - - + +
91d PRO* 1.3 63.3 - - - +
92d GLU* 3.4 1.3 - - + +
93d VAL* 4.3 19.7 - - + +
94d ARG* 3.3 12.0 + - - +
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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