Contacts of the helix formed by residues 68 - 76 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A LEU* 6.0 0.7 - - - +
49A GLN 4.4 7.2 - - - +
50A GLY 4.9 0.9 - - - -
51A GLY* 4.2 6.5 - - - +
67A GLN* 1.3 87.2 + - - +
69A SER* 1.3 65.1 + - - +
70A PHE* 2.9 36.6 + - - +
71A PHE* 2.8 32.1 + - + +
72A HIS* 2.9 25.3 + - - +
147A LEU* 4.7 5.6 - - - +
57B TYR* 3.5 47.6 - - + +
58B CYS* 4.7 8.7 - - - -
59B THR* 6.2 0.2 - - - +
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Residues in contact with SER 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A ARG* 3.0 18.0 + - - +
67A GLN 3.5 0.2 + - - -
68A GLU* 1.3 78.6 + - - +
70A PHE* 1.3 58.8 + - - +
72A HIS* 3.3 2.5 + - - +
73A TRP* 2.9 29.3 + - - +
184A ARG* 3.9 9.6 - - - -
374A ILE* 3.5 21.2 - - - +
375A ASP* 2.6 39.3 + - - -
57B TYR* 4.8 2.8 - - - -
59B THR* 4.5 5.7 - - - +
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Residues in contact with PHE 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A LEU* 4.2 7.4 - - + +
68A GLU* 2.9 30.1 + - - +
69A SER* 1.3 73.6 - - - +
71A PHE* 1.3 63.2 + - - +
73A TRP* 3.3 8.6 + - - +
74A ALA* 3.1 23.0 + - - +
147A LEU* 3.5 22.0 - - + -
158A CYS* 4.0 20.9 - - - -
177A HIS* 4.2 7.9 - + - -
180A ILE* 3.7 39.7 - - + +
181A VAL* 3.8 26.0 - - + -
184A ARG* 3.4 37.2 - - - +
379A VAL* 4.1 10.5 - - + -
58B CYS* 4.5 8.1 - - - -
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Residues in contact with PHE 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A LEU* 3.7 22.6 - - + +
49A GLN 3.8 5.2 - - - +
50A GLY* 3.5 25.6 - - - -
67A GLN* 3.5 30.3 - - + +
68A GLU* 2.8 21.7 + - + +
70A PHE* 1.3 72.9 - - - +
72A HIS* 1.3 66.7 + - - +
74A ALA* 3.3 1.6 + - - +
75A PHE* 2.9 31.1 + + + +
77A VAL* 3.8 29.6 - - + -
82A CYS* 4.0 12.6 - - + -
83A TYR* 3.6 19.1 - - - -
84A GLY* 3.3 25.4 - - - -
95A LEU* 4.1 6.7 - - + -
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Residues in contact with HIS 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A PHE* 3.1 25.5 - + - -
67A GLN* 3.9 18.4 - - + +
68A GLU 2.9 17.1 + - - +
69A SER* 3.6 7.2 - - - +
71A PHE* 1.3 77.0 - - - +
73A TRP* 1.3 62.1 + - - +
76A GLY* 2.8 35.6 + - - +
77A VAL 4.6 1.4 + - - +
78A THR* 6.1 0.4 - - - +
282A TYR* 2.9 52.8 + + - -
283A CYS* 3.5 25.4 - - + +
284A PHE* 3.6 13.9 - + - -
374A ILE* 3.8 20.4 - - + -
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Residues in contact with TRP 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A PHE* 3.4 8.5 - - - -
26A ASN* 3.0 78.1 + - + +
27A ARG 4.9 0.2 - - - -
29A ARG* 3.5 9.9 - - - +
30A LEU* 4.2 12.3 - - + -
69A SER 2.9 13.1 + - - +
70A PHE 3.3 4.7 + - - +
72A HIS* 1.3 78.0 - - - +
74A ALA* 1.3 68.1 + - + +
180A ILE* 3.7 31.4 - - + -
183A CYS* 3.4 35.9 - - + -
184A ARG* 3.5 35.1 - - + +
191A GLU* 3.2 23.5 + - - -
284A PHE* 6.3 0.2 - - - -
374A ILE* 3.3 26.2 - - + -
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Residues in contact with ALA 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A PHE* 3.6 4.8 - - - +
26A ASN* 4.8 0.2 - - - -
27A ARG* 2.9 43.7 + - + +
30A LEU* 5.8 0.4 - - + -
48A LEU* 3.9 15.0 - - + -
70A PHE 3.1 16.2 + - - +
71A PHE 3.8 0.4 - - - +
73A TRP* 1.3 93.6 - - + +
75A PHE* 1.3 76.1 + - + +
86A ILE* 4.7 5.2 - - + -
180A ILE* 5.1 0.9 - - + -
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Residues in contact with PHE 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A LEU* 4.4 1.4 - - - +
23A PHE* 3.8 12.3 - - - +
27A ARG* 3.9 25.2 + - - +
48A LEU* 4.5 7.4 - - + -
71A PHE* 2.9 31.0 + + + +
72A HIS 3.2 0.2 + - - -
74A ALA* 1.3 97.7 - - + +
76A GLY* 1.3 64.1 + - - +
77A VAL* 3.2 21.1 + - + +
84A GLY* 3.6 37.9 - - - -
85A VAL 3.7 11.0 - - - -
86A ILE* 3.9 14.8 - - + -
93A SER* 4.2 12.8 - - - -
94A THR 4.4 5.6 - - - -
95A LEU* 4.7 7.9 - - + -
121A TYR* 3.8 13.3 - - - +
123A VAL* 4.2 15.0 - - + -
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Residues in contact with GLY 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A PHE* 3.5 19.9 - - - -
71A PHE 3.9 0.2 + - - -
72A HIS* 2.8 33.6 + - - -
75A PHE* 1.3 71.4 - - - +
77A VAL* 1.3 61.9 + - - +
78A THR* 3.7 1.4 + - - +
121A TYR* 3.3 9.0 - - - -
282A TYR* 2.6 32.9 + - - -
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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