Contacts of the helix formed by residues 68 - 76 (chain B) in PDB entry 5M4G
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 GLU 68 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A TYR* 3.4 47.9 - - + +
58A CYS* 4.7 8.5 - - - -
48B LEU* 6.1 0.3 - - - +
49B GLN 4.4 7.3 - - - +
50B GLY 4.8 1.1 - - - -
51B GLY 4.1 7.4 - - - +
67B GLN* 1.3 88.5 + - - +
69B SER* 1.3 64.7 + - - +
70B PHE* 2.9 36.6 + - - +
71B PHE* 2.8 32.4 + - + +
72B HIS* 2.9 25.1 + - - +
147B LEU* 4.8 5.3 - - - +
159B ARG* 6.6 0.7 - - + -
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Residues in contact with SER 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A TYR* 4.8 2.6 - - - +
59A THR* 4.5 6.3 - - - +
66B ARG* 3.0 18.0 + - - +
67B GLN 3.6 0.4 + - - -
68B GLU* 1.3 76.0 + - - +
70B PHE* 1.3 62.6 + - - +
72B HIS* 3.7 2.5 - - - +
73B TRP* 2.9 28.8 + - - +
184B ARG* 3.8 9.3 + - - -
374B ILE* 3.5 22.3 - - - +
375B ASP* 2.6 36.3 + - - -
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Residues in contact with PHE 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A CYS* 4.6 8.3 - - - -
48B LEU* 4.2 7.4 - - + +
68B GLU* 2.9 29.9 + - - +
69B SER* 1.3 73.4 - - - +
71B PHE* 1.3 62.2 + - - +
73B TRP* 3.3 8.4 + - - +
74B ALA* 3.1 23.7 + - - +
147B LEU* 3.6 22.4 - - + -
158B CYS* 4.0 20.6 - - - -
177B HIS* 4.2 9.4 - + - -
180B ILE* 3.8 40.0 - - + +
181B VAL* 3.8 25.6 - - + -
184B ARG* 3.5 37.5 - - - +
379B VAL* 4.1 11.7 - - + -
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Residues in contact with PHE 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B LEU* 3.6 26.2 - - + +
49B GLN 3.7 4.7 - - - +
50B GLY* 3.5 23.6 - - - -
67B GLN* 3.6 28.5 - - + +
68B GLU* 2.8 25.9 + - - +
70B PHE* 1.3 72.0 - - - +
72B HIS* 1.3 57.8 + - - +
74B ALA* 3.3 2.3 + - - +
75B PHE* 2.9 42.9 + + + +
77B VAL* 3.9 28.5 - - + -
82B CYS* 4.1 10.1 - - + -
83B TYR* 3.6 20.6 - - - -
84B GLY* 3.4 23.1 - - - -
95B LEU* 4.2 3.1 - - + -
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Residues in contact with HIS 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B PHE* 3.1 23.5 - + - -
67B GLN* 3.8 17.6 - - + +
68B GLU 2.9 18.2 + - - +
69B SER* 3.7 6.5 - - - +
71B PHE* 1.3 76.6 - - - +
73B TRP* 1.3 63.5 + - - +
76B GLY* 2.8 34.7 + - - +
77B VAL 4.8 1.0 + - - +
78B THR* 6.0 0.4 - - - +
282B TYR* 2.9 53.1 + + - -
283B CYS* 3.5 24.9 - - + +
284B PHE* 3.5 14.3 - - - -
374B ILE* 3.7 20.4 - - + -
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Residues in contact with TRP 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B PHE* 3.4 8.2 - - - -
26B ASN* 2.9 84.1 + - + +
27B ARG 4.8 0.2 - - - -
29B ARG* 3.6 9.9 - - - +
30B LEU* 4.1 14.1 - - + -
69B SER 2.9 18.2 + - - +
70B PHE 3.3 4.5 + - - +
72B HIS* 1.3 83.0 - - - +
74B ALA* 1.3 68.8 + - + +
180B ILE* 3.8 29.6 - - + -
183B CYS* 3.4 34.5 - - + -
184B ARG* 3.5 36.8 - - + +
191B GLU* 3.3 19.3 + - - -
284B PHE* 6.2 0.4 - + - -
374B ILE* 4.5 13.7 - - + -
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Residues in contact with ALA 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B PHE* 3.5 4.2 - - - +
26B ASN* 4.8 0.4 - - - -
27B ARG* 2.9 42.3 + - + +
30B LEU* 5.8 0.7 - - + -
48B LEU* 3.8 15.9 - - + -
70B PHE 3.1 15.0 + - - +
71B PHE 3.9 0.2 - - - +
72B HIS 3.2 0.2 - - - -
73B TRP* 1.3 94.3 - - + +
75B PHE* 1.3 75.9 + - + +
86B ILE* 4.6 5.6 - - + -
180B ILE* 5.1 1.1 - - + -
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Residues in contact with PHE 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B LEU* 4.4 1.6 - - - +
23B PHE* 3.9 12.5 - - - +
27B ARG* 3.9 23.7 + - - +
48B LEU* 4.4 7.2 - - + -
71B PHE* 2.9 33.7 + + + +
74B ALA* 1.3 96.8 - - + +
76B GLY* 1.3 64.7 + - - +
77B VAL* 3.2 21.9 + - + +
84B GLY* 3.6 37.2 - - - -
85B VAL 3.8 9.2 - - - -
86B ILE* 3.9 13.2 - - + -
93B SER* 4.3 13.2 - - - -
94B THR 4.3 6.7 - - - -
95B LEU* 4.7 7.4 - - + -
121B TYR* 3.9 13.7 - - - +
123B VAL* 4.1 14.4 - - + -
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Residues in contact with GLY 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B PHE* 3.5 19.9 - - - -
71B PHE 3.9 0.2 + - - -
72B HIS* 2.8 34.6 + - - -
75B PHE* 1.3 70.5 - - - +
77B VAL* 1.3 62.0 + - - +
78B THR* 3.6 1.6 + - - +
121B TYR* 3.4 8.4 - - - -
282B TYR* 2.7 31.7 + - - -
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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