Contacts of the helix formed by residues 74 - 81 (chain H) in PDB entry 6CM9
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 ILE 74 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101G LEU* 5.2 7.6 - - + -
102G LEU* 4.5 13.7 - - + -
48H THR 5.0 1.3 - - - +
49H ILE* 3.2 44.9 - - + +
68H VAL* 4.1 11.0 - - + -
69H GLY 3.4 22.4 - - - +
71H LEU* 3.1 29.1 + - + +
73H LYS* 1.3 97.4 - - + +
75H ARG* 1.3 53.8 + - - +
76H PRO* 3.2 2.9 - - - -
77H LEU* 2.5 37.9 + - + +
78H TRP* 3.8 9.5 + - + +
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Residues in contact with ARG 75 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24H GLY 5.0 0.4 + - - -
25H LEU* 3.4 22.9 - - - +
26H ASP* 3.9 4.6 + - - +
70H GLY* 2.8 25.0 + - - +
71H LEU 3.4 14.6 + - - +
72H ASP* 4.2 22.9 + - - +
74H ILE* 1.3 73.8 - - - +
76H PRO* 1.3 65.7 - - + +
77H LEU 3.3 0.2 - - - -
78H TRP* 3.8 44.3 + - + +
99H ARG* 3.1 29.5 - - - +
102H GLU* 4.0 18.4 + - - +
106H GLU* 4.7 9.2 - - - +
109H ARG* 3.7 24.3 + - - +
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Residues in contact with PRO 76 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98G ASP* 5.9 1.8 - - - +
72H ASP 3.9 13.9 - - - +
73H LYS 4.4 4.7 - - - +
74H ILE 3.5 5.2 - - - +
75H ARG* 1.3 92.4 - - + +
77H LEU* 1.3 62.8 + - + +
78H TRP 3.2 5.4 + - - -
79H ARG* 3.1 36.3 + - - +
109H ARG* 5.3 6.1 - - - +
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Residues in contact with LEU 77 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98G ASP* 3.3 41.7 - - - +
99G VAL* 4.4 2.7 - - - -
101G LEU* 4.2 23.6 - - + -
102G LEU* 4.3 27.3 - - + +
73H LYS 4.5 9.6 - - - +
74H ILE* 2.5 24.9 + - + +
76H PRO* 1.3 75.6 - - + +
78H TRP* 1.3 63.3 + - - +
79H ARG* 3.1 6.9 + - - +
80H HIS* 3.3 44.2 + - + +
81H TYR* 4.5 7.1 - - - -
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Residues in contact with TRP 78 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21H LEU* 5.5 0.4 - - + -
23H VAL* 3.6 27.1 - - + -
24H GLY* 3.2 43.7 - - - -
25H LEU* 5.6 0.4 - - + -
68H VAL* 3.4 23.7 - - + +
69H GLY 3.2 25.3 + - - -
70H GLY* 3.9 5.8 - - - -
74H ILE* 3.9 11.6 - - + +
75H ARG* 4.0 27.4 - - + +
76H PRO 3.2 2.6 - - - -
77H LEU* 1.3 80.2 - - - +
79H ARG* 1.3 60.4 + - - +
80H HIS 3.1 1.3 - - - -
81H TYR* 3.1 17.9 + - - +
82H PHE* 3.3 31.6 - + + -
90H PHE* 4.5 0.2 - + - -
106H GLU* 3.2 41.7 - - + -
110H MET* 4.0 10.1 - - - -
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Residues in contact with ARG 79 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98G ASP* 5.2 4.8 + - - -
76H PRO* 3.1 36.4 + - - +
77H LEU* 5.1 4.4 - - - +
78H TRP* 1.3 76.1 - - - +
80H HIS* 1.3 90.6 + - + +
81H TYR 3.2 1.4 + - - -
82H PHE* 3.6 21.8 + - + -
113H GLU* 4.9 6.3 - - - +
115H GLU* 3.6 30.2 - - - +
288M HIS* 4.4 32.6 + - - -
364M SER* 3.8 9.6 + - - +
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Residues in contact with HIS 80 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68G LEU* 3.6 35.7 - - + +
72G LYS* 5.4 1.4 + - - -
99G VAL* 3.5 26.9 - - + +
102G LEU* 4.9 3.4 - - + -
19H ARG* 5.2 0.7 + - - -
77H LEU* 3.3 53.1 - - + +
78H TRP 3.1 1.0 - - - -
79H ARG* 1.3 103.2 + - + +
81H TYR* 1.3 68.6 + - + +
82H PHE 3.6 0.4 - - - -
83H GLN* 5.3 3.0 + - - +
364M SER* 3.7 14.0 + - - -
365M VAL* 3.9 31.7 + - + +
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Residues in contact with TYR 81 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68G LEU* 4.3 15.6 - - + +
71G LEU* 4.8 2.7 - - + +
72G LYS* 4.5 12.8 - - + -
102G LEU* 3.4 33.0 - - + +
19H ARG* 3.9 23.7 + - - +
21H LEU* 3.3 24.7 - - + +
51H PHE* 3.3 38.2 - + + -
66H TRP* 5.2 9.6 - + + -
68H VAL* 3.5 34.3 - - + -
77H LEU 4.5 9.9 - - - -
78H TRP* 3.1 9.9 + - - +
80H HIS* 1.3 88.6 - - + +
82H PHE* 1.3 51.7 + - - +
83H GLN 3.2 6.5 + - - -
85H THR* 2.7 25.6 + - - -
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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