Contacts of the helix formed by residues 73 - 85 (chain B) in PDB entry 4Z54
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 GLY 73 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B GLY 3.5 2.0 + - - -
72B LEU* 1.3 80.3 - - - +
74B LYS* 1.3 58.5 + - - +
75B SER 3.5 2.2 - - - -
76B THR* 3.4 2.3 + - - -
77B LEU* 2.9 31.0 + - - +
177B PHE* 4.1 3.6 - - - -
208B LYS* 4.3 0.2 - - - +
265B GLY* 5.8 0.3 - - - -
401B GDP 2.9 46.2 + - - -
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Residues in contact with LYS 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B VAL* 4.1 13.2 - - + +
67B VAL 3.5 14.8 - - - +
68B GLY* 3.4 39.2 + - - +
69B GLN 2.9 20.2 + - - +
70B SER* 3.8 5.7 - - - +
72B LEU* 4.7 1.1 - - + -
73B GLY* 1.3 78.1 - - - +
75B SER* 1.3 57.1 + - - +
77B LEU* 3.1 3.8 + - - +
78B VAL* 2.9 32.9 + - - +
125B ASP* 4.4 2.2 - - - +
126B THR* 3.8 28.0 + - - -
127B PRO 4.6 1.3 - - - -
128B GLY* 4.3 3.6 - - - +
177B PHE* 3.8 29.8 - - + -
401B GDP 2.8 36.6 + - - +
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Residues in contact with SER 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B LYS* 1.3 73.2 - - - +
76B THR* 1.3 66.9 + - - +
78B VAL* 3.2 5.5 + - - +
79B ASN* 3.1 25.8 + - - +
99B ILE* 3.6 26.2 - - - -
102B THR* 2.7 3.9 + - - -
125B ASP* 2.6 30.1 + - - -
401B GDP 3.0 7.9 + - - -
402B MG 2.1 31.1 - - - -
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Residues in contact with THR 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B GLY 3.6 6.1 - - - -
74B LYS 3.2 0.2 - - - -
75B SER* 1.3 77.0 - - - +
77B LEU* 1.3 56.0 + - - +
79B ASN* 3.2 4.9 + - - +
80B THR* 2.7 28.9 + - - -
99B ILE* 3.7 21.5 - - + +
265B GLY* 3.5 31.0 - - - +
266B SER* 3.6 11.2 - - - +
267B ASP* 4.4 3.8 - - - +
401B GDP 2.7 52.1 + - + +
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Residues in contact with LEU 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B VAL* 5.5 2.7 - - + -
73B GLY 2.9 16.9 + - - +
74B LYS 3.1 4.7 + - - +
76B THR* 1.3 73.8 - - - +
78B VAL* 1.3 66.3 + - - +
80B THR* 3.4 3.1 - - - -
81B LEU* 2.9 25.2 + - + +
175B LEU* 4.4 10.1 - - + -
177B PHE* 3.5 28.3 - - + -
205B VAL* 5.1 0.7 - - + -
263B VAL* 4.0 17.9 - - + -
264B VAL 4.0 2.9 - - - +
265B GLY* 3.8 24.4 - - - +
297B PHE* 3.9 26.2 - - + -
300B LEU* 4.1 25.4 - - + -
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Residues in contact with VAL 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B VAL* 3.7 27.3 - - + +
74B LYS 2.9 19.7 + - - +
75B SER* 3.3 9.2 - - - +
77B LEU* 1.3 77.0 - - - +
79B ASN* 1.3 69.0 + - - +
81B LEU* 3.3 5.4 + - - +
82B PHE* 3.2 38.1 + - + -
108B ILE* 4.6 13.9 - - + -
123B VAL* 3.7 30.4 - - + +
125B ASP* 4.1 15.3 - - + +
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Residues in contact with ASN 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B SER* 3.1 11.0 + - - +
76B THR 3.2 6.0 + - - +
78B VAL* 1.3 85.8 - - - +
80B THR* 1.3 57.5 + - - +
82B PHE* 3.3 10.0 + - - +
83B LYS* 2.9 30.5 + - - +
99B ILE* 3.4 20.4 - - - +
267B ASP* 3.1 37.2 + - + +
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Residues in contact with THR 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B THR 2.7 18.2 + - - -
77B LEU* 3.2 13.4 + - - -
79B ASN* 1.3 74.2 - - - +
81B LEU* 1.3 60.5 + - - +
83B LYS* 3.2 2.5 + - - -
84B SER* 2.9 28.8 + - - -
265B GLY* 3.6 4.2 - - - -
266B SER 2.8 38.2 + - - +
267B ASP* 4.6 0.2 - - - +
278B LEU* 3.7 8.3 - - + +
289B VAL* 3.6 30.3 - - + -
297B PHE* 3.7 16.8 - - + -
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Residues in contact with LEU 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ILE* 3.6 33.0 - - + -
77B LEU* 2.9 13.4 + - + +
78B VAL* 3.5 9.9 - - - +
80B THR* 1.3 76.4 - - - +
82B PHE* 1.3 61.4 + - - +
84B SER* 2.7 27.0 + - - +
85B GLN* 3.5 9.2 + - - +
121B LEU* 4.5 8.8 - - + +
123B VAL* 3.9 21.8 - - + -
175B LEU* 5.9 5.2 - - + -
297B PHE* 3.9 18.8 - - + -
300B LEU* 6.4 1.8 - - + -
301B ARG* 4.6 10.5 - - + -
304B VAL* 6.3 1.1 - - + -
305B ILE* 3.7 25.1 - - + -
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Residues in contact with PHE 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B VAL* 3.2 25.5 + - + -
79B ASN* 3.7 11.7 - - - +
80B THR 3.2 0.2 - - - -
81B LEU* 1.3 79.3 - - - +
83B LYS* 1.3 59.5 + - - +
84B SER 3.5 0.5 + - - -
85B GLN* 3.5 7.8 + - + +
86B VAL* 3.0 28.1 + - + +
108B ILE* 3.2 49.1 - - + -
110B HIS* 4.0 25.1 + + + -
112B ILE* 6.3 0.2 - - + -
121B LEU* 3.9 28.0 - - + -
123B VAL* 3.4 33.7 - - + -
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Residues in contact with LYS 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B ASN 2.9 16.8 + - - +
80B THR* 3.2 4.5 + - - +
82B PHE* 1.3 74.1 - - - +
84B SER* 1.3 63.0 + - - +
85B GLN 3.3 0.2 - - - -
86B VAL* 4.1 15.3 + - - +
267B ASP* 5.2 6.7 - - + +
269B GLU* 6.1 0.7 - - - +
278B LEU* 3.8 30.1 - - + +
290B GLU* 4.9 0.7 - - - +
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Residues in contact with SER 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B THR 2.9 13.0 + - - -
81B LEU* 2.7 20.6 + - - +
83B LYS* 1.3 79.5 - - - +
85B GLN* 1.3 69.8 + - - +
86B VAL 3.4 7.6 + - - +
278B LEU* 4.2 1.3 - - - -
290B GLU* 3.3 35.1 - - - +
297B PHE* 3.9 10.8 - - - -
301B ARG* 3.7 16.1 - - - +
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Residues in contact with GLN 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B LEU 3.5 8.1 + - - +
82B PHE* 3.5 3.7 + - - +
83B LYS 3.3 0.4 - - - -
84B SER* 1.3 85.4 + - - +
86B VAL* 1.3 65.1 + - - +
110B HIS* 5.3 2.1 - - - -
112B ILE* 3.6 43.3 - - + +
121B LEU* 5.3 1.3 - - + -
301B ARG* 4.2 20.4 - - - +
305B ILE* 3.7 44.4 - - + +
306B ARG* 4.8 16.8 + - - +
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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