Contacts of the helix formed by residues 60 - 74 (chain Q) in PDB entry 6P19
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 60 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395D LYS* 5.1 3.6 + - - -
399D LYS* 4.1 30.3 - - + -
403D ARG* 6.3 0.2 - - - +
26Q TRP* 2.5 50.0 + - + -
58Q CYS* 3.2 15.4 - - - +
59Q ASN* 1.3 78.0 + - - +
61Q ASP* 1.3 62.4 + - - +
62Q ASP* 3.1 5.1 + - - -
63Q GLY 4.1 0.2 - - - +
64Q MET* 2.9 34.5 + - - +
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Residues in contact with ASP 61 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
860C ALA* 3.3 26.0 - - + +
399D LYS* 6.1 0.2 - - - +
403D ARG* 4.0 22.0 + - - -
59Q ASN* 2.8 13.4 + - + +
60Q ASP* 1.3 82.0 - - - +
62Q ASP* 1.3 59.8 + - - +
63Q GLY 3.2 0.7 - - - -
64Q MET* 3.1 9.3 + - - +
65Q LEU* 2.9 33.1 + - - +
152Q ARG* 4.0 17.5 + - - +
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Residues in contact with ASP 62 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19Q TRP* 4.5 25.5 - - + -
22Q LEU* 5.4 0.3 - - - +
58Q CYS* 3.3 19.2 - - - +
59Q ASN* 3.4 11.3 + - - +
60Q ASP 3.1 20.3 + - - -
61Q ASP* 1.3 71.0 + - - +
63Q GLY* 1.3 61.6 + - - -
65Q LEU* 3.3 16.1 - - + +
66Q ILE* 3.0 36.6 + - - +
149Q PHE* 6.2 0.9 - - + -
152Q ARG* 4.6 8.2 - - - +
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Residues in contact with GLY 63 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26Q TRP* 3.5 20.6 - - - -
58Q CYS* 3.7 15.6 - - - +
60Q ASP 3.8 1.6 - - - -
61Q ASP 3.2 0.2 - - - -
62Q ASP* 1.3 86.9 + - - +
64Q MET* 1.3 52.9 + - - +
66Q ILE* 3.4 11.0 - - - +
67Q SER* 2.3 41.1 + - - -
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Residues in contact with MET 64 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396D ALA* 4.9 13.9 - - - +
399D LYS* 3.6 33.0 - - + +
400D MET* 3.7 35.9 - - + -
403D ARG* 5.4 4.7 - - + +
26Q TRP* 4.6 6.1 - - + -
60Q ASP* 2.9 26.2 + - + +
61Q ASP* 3.1 12.5 + - - +
63Q GLY* 1.3 75.9 - - - +
65Q LEU* 1.3 57.8 + - - +
67Q SER* 3.4 6.4 + - - -
68Q GLN* 2.9 30.0 + - + +
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Residues in contact with LEU 65 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61Q ASP 2.9 19.6 + - - +
62Q ASP* 3.3 18.2 - - + +
64Q MET* 1.3 76.5 - - - +
66Q ILE* 1.3 75.0 + - + +
68Q GLN* 3.2 10.3 + - - +
69Q VAL* 3.0 33.0 + - + +
145Q LEU* 4.9 3.8 - - + -
148Q ALA* 4.3 28.7 - - + +
149Q PHE* 5.2 7.4 - - + +
152Q ARG* 3.7 38.4 - - - +
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Residues in contact with ILE 66 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19Q TRP* 4.5 28.9 - - + +
20Q LEU* 5.4 7.2 - - + -
22Q LEU* 5.9 1.8 - - + -
23Q TRP* 3.6 41.5 - - + -
58Q CYS* 6.0 0.2 - - - -
62Q ASP 3.0 21.2 + - - +
63Q GLY* 3.4 11.7 - - - +
65Q LEU* 1.3 82.6 - - + +
67Q SER* 1.3 63.4 + - - +
69Q VAL* 3.2 10.0 - - + +
70Q VAL* 3.0 33.8 + - + +
145Q LEU* 3.7 31.0 - - + -
149Q PHE* 6.2 1.3 - - + -
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Residues in contact with SER 67 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392D THR* 5.7 0.7 - - - -
393D THR* 5.6 4.6 - - - +
396D ALA* 5.1 13.5 - - - -
23Q TRP* 3.2 21.8 + - - +
26Q TRP* 3.3 10.8 - - - -
27Q VAL* 5.2 0.3 - - - +
63Q GLY 2.3 27.2 + - - -
64Q MET* 3.7 7.4 - - - -
66Q ILE* 1.3 76.3 - - - +
68Q GLN* 1.3 58.4 + - - +
70Q VAL* 3.3 9.5 - - - +
71Q ASP* 2.9 41.1 + - - +
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Residues in contact with GLN 68 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64Q MET* 2.9 19.0 + - + +
65Q LEU* 3.5 9.0 - - - +
66Q ILE 3.2 0.2 - - - -
67Q SER* 1.3 77.7 - - - +
69Q VAL* 1.3 74.9 + - - +
71Q ASP* 3.4 6.8 + - - +
72Q SER* 2.9 34.3 + - - -
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Residues in contact with VAL 69 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65Q LEU* 3.0 14.4 + - + +
66Q ILE* 3.2 24.9 - - + +
68Q GLN* 1.3 88.8 - - - +
70Q VAL* 1.3 58.1 + - + +
72Q SER* 2.7 21.4 + - - +
73Q VAL* 3.0 19.6 + - - +
141Q ILE* 3.8 19.3 - - + -
144Q VAL* 4.8 15.9 - - + -
145Q LEU* 4.6 16.6 - - + -
148Q ALA* 4.1 23.8 - - + -
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Residues in contact with VAL 70 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20Q LEU* 5.5 7.9 - - + -
23Q TRP* 3.8 32.5 - - + -
66Q ILE* 3.0 18.2 + - + +
67Q SER* 3.3 20.4 - - - +
69Q VAL* 1.3 76.2 - - + +
71Q ASP* 1.3 64.5 + - - +
73Q VAL* 4.2 2.5 - - - -
74Q MET* 2.9 43.1 + - + +
81Q PHE* 4.4 10.1 - - + -
84Q LEU* 6.1 2.7 - - + -
141Q ILE* 3.7 26.2 - - + -
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Residues in contact with ASP 71 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389D GLY 5.3 3.4 - - - +
390D LEU 3.9 15.1 - - - +
392D THR* 2.7 47.1 + - + +
67Q SER* 2.9 30.1 + - - +
68Q GLN* 3.7 6.9 - - - +
69Q VAL 3.3 0.2 - - - -
70Q VAL* 1.3 85.4 - - - +
72Q SER* 1.3 63.0 + - - +
74Q MET 5.3 0.4 - - - -
75Q TYR* 3.9 25.0 + - + +
81Q PHE* 4.4 5.1 - - - -
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Residues in contact with SER 72 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68Q GLN* 2.9 22.0 + - - -
69Q VAL* 2.7 26.0 + - - +
71Q ASP* 1.3 81.4 - - - +
73Q VAL* 1.3 59.9 + - - +
75Q TYR* 4.3 7.6 + - - +
144Q VAL* 6.0 1.4 - - - +
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Residues in contact with VAL 73 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69Q VAL 3.0 20.6 + - - +
72Q SER* 1.3 78.9 + - - +
74Q MET* 1.3 90.3 + - + +
75Q TYR 3.3 6.3 + - - -
76Q ILE* 3.6 21.5 - - + +
140Q MET* 4.5 18.6 - - + +
141Q ILE* 3.7 25.4 - - + -
144Q VAL* 5.4 5.2 - - + -
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Residues in contact with MET 74 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70Q VAL* 2.9 34.2 + - + +
71Q ASP* 4.4 1.3 - - - -
72Q SER 3.6 0.2 - - - -
73Q VAL* 1.3 118.8 - - + +
75Q TYR* 1.3 59.0 + - - +
76Q ILE* 3.4 4.3 - - + +
77Q ASP* 3.5 26.8 - - + +
80Q ALA* 5.4 5.6 - - - -
81Q PHE* 4.1 28.1 - - + -
84Q LEU* 4.8 11.9 - - + -
137Q SER* 3.8 37.7 - - - +
140Q MET* 4.6 10.8 - - + -
141Q ILE* 5.4 2.9 - - + -
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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