Contacts of the helix formed by residues 75 - 89 (chain e) in PDB entry 5GJQ
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 SER 75 (chain e).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100E ASP* 3.1 26.1 + - - -
41e LEU* 5.4 0.4 - - - -
66e TYR* 5.1 0.6 - - - -
73e ARG 3.5 2.5 + - - -
74e ILE* 1.3 79.7 - - - +
76e VAL* 1.3 67.0 + - - +
77e ALA* 3.6 3.3 + - - +
78e ALA* 3.0 21.6 + - - +
79e ALA* 3.0 22.3 + - - +
105e ASP* 3.1 27.8 - - - -
107e ARG* 4.0 5.8 - - - -
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Residues in contact with VAL 76 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41e LEU* 4.4 10.5 - - + -
74e ILE 5.7 0.2 - - - +
75e SER* 1.3 75.6 - - - +
77e ALA* 1.3 57.3 + - - +
79e ALA* 3.2 7.0 + - - +
80e SER* 3.0 29.2 + - - -
101e ILE* 3.9 24.6 - - + +
102e CYS 4.5 0.9 - - - -
103e GLY* 3.8 33.0 - - - +
104e TRP 4.0 3.1 - - - +
105e ASP* 3.3 22.6 + - + +
110e GLY* 3.9 17.9 - - - +
112e TYR* 3.7 21.5 - - + -
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Residues in contact with ALA 77 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99E GLU* 4.8 10.1 - - + -
75e SER* 3.2 1.7 + - - +
76e VAL* 1.3 79.9 - - - +
78e ALA* 1.3 56.4 + - - +
80e SER* 2.9 19.7 + - - -
81e LYS* 2.9 15.1 + - - +
105e ASP* 4.4 1.2 + - - -
107e ARG* 3.9 27.8 - - - +
112e TYR* 3.5 24.8 - - + +
120e ARG* 3.0 17.7 + - - +
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Residues in contact with ALA 78 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97E THR 4.4 2.3 - - - +
98E VAL* 3.8 36.7 - - + +
99E GLU 5.1 0.4 - - - +
100E ASP* 4.3 0.8 + - - +
66e TYR* 5.6 1.8 - - - +
74e ILE* 3.6 22.0 - - + -
75e SER* 3.0 21.0 + - - +
77e ALA* 1.3 74.4 - - - +
79e ALA* 1.3 61.1 + - - +
81e LYS* 3.5 6.4 + - - +
82e LEU* 2.9 31.7 + - - +
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Residues in contact with ALA 79 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41e LEU* 3.9 27.4 - - + -
59e LEU* 3.6 20.7 - - + +
63e CYS* 4.3 2.5 - - - -
74e ILE* 4.1 10.7 - - + +
75e SER 3.0 16.4 + - - +
76e VAL* 3.2 5.8 + - - +
78e ALA* 1.3 79.3 - - - +
80e SER* 1.3 63.2 + - - +
82e LEU* 3.1 8.2 + - - +
83e LEU* 2.9 20.8 + - - +
101e ILE* 4.5 3.8 - - + -
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Residues in contact with SER 80 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76e VAL 3.0 13.2 + - - -
77e ALA 2.9 17.0 + - - -
79e ALA* 1.3 76.1 - - - +
81e LYS* 1.3 55.9 + - - +
83e LEU* 3.4 2.6 + - - +
84e ALA* 3.0 30.7 + - - +
101e ILE* 4.4 11.1 - - - +
112e TYR* 3.4 35.6 - - - -
114e VAL* 3.9 17.6 - - - +
120e ARG* 3.1 13.8 + - - -
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Residues in contact with LYS 81 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96E LEU* 2.5 34.9 + - - +
97E THR 3.5 18.4 - - - +
98E VAL* 4.8 2.5 - - - +
99E GLU* 4.4 9.5 + - - +
54d VAL* 4.7 7.4 - - - -
55d GLN* 5.1 2.7 - - - +
58d GLU* 2.3 36.2 + - - -
77e ALA 2.9 19.9 + - - +
78e ALA* 3.7 6.1 - - - +
80e SER* 1.3 75.9 + - - +
82e LEU* 1.3 57.5 + - - +
84e ALA* 3.8 2.1 - - - +
85e ASN* 2.9 57.1 + - - +
120e ARG* 3.3 32.1 - - - +
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Residues in contact with LEU 82 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97E THR* 4.7 8.7 + - - +
98E VAL* 5.9 3.6 - - + -
59e LEU* 4.0 10.8 - - + -
62e GLN* 3.9 36.8 - - + -
66e TYR* 6.1 1.3 - - + -
74e ILE* 3.8 30.1 - - + -
78e ALA* 2.9 11.6 + - + +
79e ALA 3.2 9.4 - - - +
81e LYS* 1.3 74.0 - - - +
83e LEU* 1.3 64.8 + - - +
85e ASN* 3.3 8.6 + - + +
86e MET* 3.0 40.7 + - + +
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Residues in contact with LEU 83 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55e TRP* 3.8 29.6 - - + +
56e GLU* 4.1 7.2 - - + -
59e LEU* 4.3 11.4 - - + +
79e ALA 2.9 12.3 + - - +
80e SER* 3.7 8.5 - - - +
82e LEU* 1.3 72.8 - - - +
84e ALA* 1.3 67.8 + - - +
86e MET* 3.2 12.8 + - + +
87e VAL* 3.0 27.2 + - + +
97e MET* 3.6 33.2 - - + -
99e THR* 3.7 17.0 - - + -
101e ILE* 3.8 21.1 - - + -
114e VAL* 3.9 9.6 - - + -
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Residues in contact with ALA 84 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55d GLN* 4.7 5.1 + - - +
80e SER 3.0 15.1 + - - +
81e LYS* 3.8 4.7 - - + +
83e LEU* 1.3 81.1 - - - +
85e ASN* 1.3 59.5 + - - +
87e VAL* 3.3 6.7 + - - +
88e TYR* 2.9 30.3 + - - +
114e VAL* 4.2 8.6 - - + +
115e ASP 5.4 0.4 - - - -
118e GLY* 4.2 15.2 - - - +
119e ASN 4.5 4.3 - - - +
120e ARG* 4.2 24.9 - - + -
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Residues in contact with ASN 85 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96E LEU* 5.2 1.4 - - - +
97E THR* 4.3 20.0 + - - +
55d GLN* 3.0 30.7 + - - +
81e LYS* 2.9 53.4 + - - +
82e LEU* 3.7 8.4 - - + +
83e LEU 3.3 0.2 - - - -
84e ALA* 1.3 71.0 - - - +
86e MET* 1.3 66.8 + - + +
87e VAL 3.5 0.2 + - - -
88e TYR* 3.5 12.7 + - - +
89e GLN* 3.9 15.2 + - - +
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Residues in contact with MET 86 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55e TRP* 4.0 36.4 - - + +
58e LEU* 4.1 26.0 - - + +
59e LEU* 4.0 18.8 - - + +
62e GLN* 5.4 8.7 - - + +
82e LEU* 3.0 34.1 + - + +
83e LEU* 3.7 17.5 - - + +
85e ASN* 1.3 81.1 - - + +
87e VAL* 1.3 62.8 + - - +
89e GLN* 3.6 15.5 + - - +
90e TYR* 3.8 17.0 - - - -
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Residues in contact with VAL 87 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55e TRP* 4.1 24.5 - - + -
83e LEU* 3.0 18.5 + - + +
84e ALA* 4.2 5.4 - - - +
86e MET* 1.3 74.1 - - - +
88e TYR* 1.3 65.2 + - - +
89e GLN 3.1 4.1 + - - -
90e TYR* 3.2 21.2 + - - +
91e LYS 3.9 2.9 + - - -
95e LEU* 4.3 14.1 - - + +
97e MET* 4.1 26.2 - - + -
114e VAL* 5.7 0.2 - - + -
115e ASP 3.6 24.5 - - - +
116e SER* 3.8 21.8 - - - +
118e GLY* 5.2 2.9 - - - +
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Residues in contact with TYR 88 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51d GLY* 4.2 11.7 - - - -
52d ASP* 3.1 25.9 + - - -
55d GLN* 3.6 48.7 - - + +
96d THR* 5.2 8.8 + - - -
97d PRO 4.8 3.8 + - - -
98d TYR* 3.4 31.7 - - - -
84e ALA 2.9 17.6 + - - +
85e ASN 3.9 5.8 - - - +
86e MET 3.3 1.0 - - - -
87e VAL* 1.3 78.0 - - - +
89e GLN* 1.3 67.5 + - + +
90e TYR 3.1 1.3 + - - -
91e LYS* 3.2 36.8 + - + +
116e SER 5.6 0.9 - - - -
117e GLU 4.8 3.1 - - - -
118e GLY* 5.1 6.7 - - - -
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Residues in contact with GLN 89 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85e ASN 3.9 14.3 + - - +
86e MET* 3.6 12.4 + - - +
87e VAL 3.1 1.2 - - - -
88e TYR* 1.3 84.1 - - + +
90e TYR* 1.3 73.7 + - + +
91e LYS 3.4 3.3 - - - +
93e MET* 4.9 8.3 - - - +
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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
------------------------------------------------------------
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