Contacts of the helix formed by residues 77 - 93 (chain K) in PDB entry 5A0Q
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 77 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41K LYS 4.4 3.6 - - - +
42K ILE* 4.8 4.0 - - + -
75K LEU 4.4 2.2 - - - +
76K SER* 1.3 86.8 - - - +
78K THR* 1.3 55.6 + - + +
80K ALA* 4.7 1.6 - - + -
81K ALA* 3.1 16.7 + - - +
104K LEU* 3.1 31.4 - - + +
106K GLY* 3.4 18.6 - - - +
107K TYR 3.3 29.4 - - - +
108K ASP* 3.5 26.7 - - + +
111K GLU* 5.0 1.8 - - - +
114K ALA* 4.2 13.5 - - + +
116K TYR* 4.3 7.6 - - + -
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Residues in contact with THR 78 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C GLN 5.7 2.4 + - - -
103C GLU* 5.3 0.9 + - - -
76K SER* 3.5 13.5 - - - -
77K PRO* 1.3 76.0 - - + +
79K ALA* 1.3 60.3 + - - +
81K ALA* 3.2 6.2 + - - +
82K ASN* 2.8 44.6 + - - +
111K GLU* 3.4 29.9 + - - +
114K ALA* 5.3 0.2 - - + -
116K TYR* 2.3 37.7 - - + +
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Residues in contact with ALA 79 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C TYR* 3.5 26.4 - - + +
102C GLN 5.5 0.9 - - - -
103C GLU* 3.6 27.8 - - + +
75K LEU* 3.8 16.8 - - + -
76K SER* 3.0 20.9 + - - +
78K THR* 1.3 81.0 + - - +
80K ALA* 1.3 61.7 + - - +
82K ASN 3.6 0.2 + - - -
83K PHE* 3.2 21.5 + - - +
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Residues in contact with ALA 80 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C TYR* 5.2 1.6 - - - -
42K ILE* 3.7 37.0 - - + -
60K ILE* 5.2 1.6 - - + +
64K VAL* 4.7 13.7 - - + -
75K LEU* 4.6 4.6 - - + +
76K SER 3.0 13.4 + - - +
77K PRO 3.9 1.6 - - - +
79K ALA* 1.3 76.7 - - - +
81K ALA* 1.4 56.3 + - - +
83K PHE* 3.3 11.9 + - - +
84K THR* 3.1 28.9 + - - +
104K LEU* 3.8 8.8 - - + +
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Residues in contact with ALA 81 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77K PRO 3.1 19.9 + - - +
78K THR* 3.4 9.4 - - - +
80K ALA* 1.4 72.7 - - - +
82K ASN* 1.3 58.6 + - - +
83K PHE 3.1 1.6 - - - -
84K THR* 3.1 5.2 - - - +
85K ARG* 3.0 28.2 + - - +
104K LEU* 3.7 3.3 - - + +
116K TYR* 4.3 10.3 - - + -
118K MET* 3.5 29.1 - - + +
124K LEU* 3.9 15.9 - - + +
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Residues in contact with ASN 82 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100C GLN 3.0 21.2 - - - +
101C TYR 3.8 6.0 + - - +
102C GLN* 3.4 33.0 + - + +
64J GLN* 4.0 0.3 + - - -
78K THR* 2.8 35.4 + - - +
81K ALA* 1.3 71.3 - - - +
83K PHE* 1.3 63.1 + - - +
85K ARG* 3.1 33.4 + - - +
86K ARG* 3.2 21.5 + - - +
116K TYR* 6.3 0.4 - - - -
124K LEU* 3.5 12.9 - - - +
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Residues in contact with PHE 83 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C GLN* 3.6 20.2 + - + -
101C TYR* 3.8 36.6 - + + -
60K ILE* 4.1 17.9 - - + -
63K ASN* 3.6 42.4 - - + -
64K VAL* 4.0 22.7 - - + -
79K ALA 3.2 14.7 + - - +
80K ALA 3.3 9.6 - - - +
81K ALA 3.1 0.8 - - - -
82K ASN* 1.3 77.0 - - - +
84K THR* 1.4 58.0 + - - +
86K ARG* 3.2 16.6 + - + +
87K ASN* 2.8 38.4 - - - +
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Residues in contact with THR 84 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44K LEU* 4.8 3.4 - - + +
56K PHE* 2.7 32.9 - - - -
60K ILE* 4.2 14.4 - - - -
80K ALA 3.1 14.2 + - - +
81K ALA* 3.1 19.7 - - - +
83K PHE* 1.4 72.8 - - - +
85K ARG* 1.3 63.0 + - - +
87K ASN* 3.2 12.4 + - - +
88K LEU* 3.1 27.3 + - - +
102K LEU* 5.8 0.2 - - - +
104K LEU* 4.0 7.9 - - + -
118K MET* 3.6 31.3 - - + -
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Residues in contact with ARG 85 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C GLN* 3.9 1.0 - - - +
60J GLN* 3.3 40.5 - - - +
64J GLN* 1.9 41.4 - - - +
81K ALA 3.0 17.8 + - - +
82K ASN* 3.1 24.4 + - - +
84K THR* 1.3 79.0 - - - +
86K ARG* 1.3 97.0 + - - +
88K LEU* 3.4 6.2 + - - -
89K ALA* 3.2 21.7 + - + +
118K MET* 5.7 4.9 - - + -
122K ALA* 3.7 16.1 - - + +
124K LEU* 3.0 38.5 - - + +
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Residues in contact with ARG 86 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C LEU* 3.7 16.0 + - - +
100C GLN* 3.8 31.4 - - + +
102C GLN* 4.6 0.4 - - - +
61J THR* 4.8 8.5 + - - +
64J GLN* 2.9 27.0 + - - +
65J ARG* 5.0 17.5 - - - +
82K ASN 3.2 10.7 + - - +
83K PHE* 3.2 12.9 + - + +
85K ARG* 1.3 134.8 - - - +
87K ASN* 1.3 61.1 + - - +
89K ALA* 3.4 14.0 + - - +
90K ASP* 2.8 38.2 + - - +
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Residues in contact with ASN 87 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56K PHE* 4.1 13.0 - - + -
59K TYR* 3.3 34.1 + - + -
60K ILE* 3.0 26.0 - - + +
83K PHE* 2.8 36.1 - - - +
84K THR* 3.2 7.1 + - - +
86K ARG* 1.3 79.7 - - - +
88K LEU* 1.3 63.1 + - - +
90K ASP* 3.2 13.1 + - - +
91K CYS* 3.1 27.7 + - - -
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Residues in contact with LEU 88 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56K PHE* 3.2 36.1 - - + -
84K THR* 3.1 19.3 + - - +
85K ARG* 4.0 1.6 - - - +
86K ARG 3.3 0.2 - - - -
87K ASN* 1.3 78.8 - - - +
89K ALA* 1.3 59.5 + - - +
91K CYS* 3.4 5.3 + - + +
92K LEU* 3.2 17.5 + - - +
98K TYR* 4.4 17.3 - - + +
100K VAL* 3.9 26.7 - - + +
102K LEU* 6.2 1.3 - - + -
118K MET* 5.1 11.4 - - + -
119K ASP 3.8 19.1 - - - +
120K TYR 4.0 11.9 - - - +
121K LEU 3.5 6.9 - - - +
122K ALA* 3.5 18.6 - - + -
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Residues in contact with ALA 89 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57J THR* 5.2 5.2 - - - +
61J THR* 4.1 19.5 - - + +
65J ARG* 5.5 5.8 - - - +
102J TYR* 5.7 1.6 + - - -
85K ARG* 3.2 17.5 + - + +
86K ARG* 3.8 15.0 - - - +
87K ASN 3.2 0.2 - - - -
88K LEU* 1.3 73.6 - - - +
90K ASP* 1.3 66.7 + - - +
92K LEU* 3.5 15.4 + - - +
93K ARG* 4.0 6.9 + - - +
121K LEU 4.1 3.4 - - - -
122K ALA* 3.5 12.3 - - + +
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Residues in contact with ASP 90 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65J ARG* 3.6 22.2 + - - +
86K ARG* 2.8 28.5 - - - +
87K ASN* 3.2 13.3 + - - +
89K ALA* 1.3 75.5 - - - +
91K CYS* 1.3 65.7 + - - +
92K LEU 3.4 0.3 + - - -
93K ARG* 3.6 7.7 + - - +
94K SER* 2.8 23.2 + - - +
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Residues in contact with CYS 91 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59K TYR* 6.0 3.8 - - - -
87K ASN* 3.1 22.1 + - - +
88K LEU* 3.4 7.6 + - + +
89K ALA 3.3 0.2 - - - -
90K ASP* 1.3 78.1 - - - +
92K LEU* 1.3 63.1 + - - +
93K ARG 3.3 0.2 - - - -
94K SER* 3.2 17.7 + - - -
96K THR* 3.1 22.8 - - - +
97K PRO* 3.1 17.3 - - - +
98K TYR* 3.7 43.3 - - + +
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Residues in contact with LEU 92 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55J LEU* 5.6 5.8 - - + -
57J THR* 4.3 18.8 - - + +
58J ASP* 5.7 1.1 - - - +
88K LEU 3.2 11.7 + - - +
89K ALA* 3.6 12.1 - - - +
90K ASP 3.2 0.8 - - - -
91K CYS* 1.3 78.8 - - - +
93K ARG* 1.3 58.8 + - - +
94K SER 3.6 3.8 + - - +
97K PRO* 4.1 18.9 - - + +
98K TYR 6.0 1.1 - - - +
99K HIS* 6.6 0.2 - - + -
120K TYR* 5.1 3.8 - - + +
121K LEU* 3.5 51.1 - - + +
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Residues in contact with ARG 93 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97J LYS* 3.9 23.4 - - - +
99J PHE* 4.7 4.0 - - - +
100J GLY* 3.5 43.2 + - - +
102J TYR* 4.1 31.9 - - + +
89K ALA 4.0 6.0 + - - +
90K ASP* 3.6 8.6 + - - +
91K CYS 3.3 0.2 - - - -
92K LEU* 1.3 76.8 - - - +
94K SER* 1.4 61.2 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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