Contacts of the helix formed by residues 90 - 100 (chain A) in PDB entry 3CMM
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 LYS 90 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A ASP 4.1 7.9 - - - +
68A PRO* 3.2 33.2 - - + +
69A GLU 3.5 5.2 - - - -
70A PRO* 5.4 1.3 - - + -
71A VAL* 4.4 0.2 - - - -
88A GLY 5.8 0.2 - - - +
89A GLN* 1.3 74.1 - - - +
91A ARG* 1.3 66.2 + - - +
92A GLY 3.3 0.2 - - - -
93A ASP* 3.1 43.9 + - - +
94A VAL* 3.3 11.8 + - - +
112A ASP* 5.4 10.0 + - - -
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Residues in contact with ARG 91 (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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44A LEU* 3.4 22.0 - - - +
45A LYS* 3.5 29.7 - - - +
67A ASP* 2.7 31.2 + - + +
69A GLU* 2.9 43.5 + - - +
70A PRO 3.7 11.7 + - - -
71A VAL* 3.6 24.7 - - + -
72A GLN* 5.3 1.8 - - - +
75A ASP* 2.6 41.2 + - - -
82A LEU* 4.4 10.5 - - + +
89A GLN 3.5 1.4 + - - -
90A LYS* 1.3 70.9 - - - +
92A GLY* 1.3 60.2 + - - +
94A VAL* 3.4 2.1 + - - +
95A THR* 2.7 33.7 + - - +
131A THR* 3.9 6.7 - - - +
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Residues in contact with GLY 92 (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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44A LEU* 5.1 1.1 - - - -
65A VAL* 4.0 21.2 - - - +
67A ASP* 2.9 28.7 + - - +
91A ARG* 1.3 71.8 - - - +
93A ASP* 1.3 62.2 + - - +
94A VAL 3.2 0.2 + - - -
95A THR* 3.3 1.8 + - - -
96A ARG* 3.0 27.5 + - - +
110A VAL* 3.5 11.6 - - - +
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Residues in contact with ASP 93 (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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89A GLN* 5.8 2.5 - - + -
90A LYS* 3.1 49.4 + - + +
92A GLY* 1.3 75.7 - - - +
94A VAL* 1.3 64.0 + - + +
96A ARG* 3.8 14.1 + - - +
97A ALA* 4.2 6.4 + - - +
110A VAL* 3.8 25.1 - - - +
112A ASP* 5.0 1.9 - - - +
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Residues in contact with VAL 94 (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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71A VAL* 4.9 1.6 - - + -
81A PHE 4.3 4.7 - - - +
82A LEU* 4.0 15.3 - - + -
86A ASP* 3.3 44.6 - - + +
89A GLN* 3.7 35.2 - - + +
90A LYS 3.3 9.3 + - - +
91A ARG* 4.0 3.8 - - - +
92A GLY 3.2 0.8 - - - -
93A ASP* 1.3 78.2 - - + +
95A THR* 1.3 60.7 + - - +
97A ALA* 4.4 3.8 + - - +
98A LYS* 3.7 20.5 + - + +
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Residues in contact with THR 95 (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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44A LEU* 3.6 22.1 - - + +
49A VAL* 3.4 32.8 - - + -
79A GLN* 3.2 16.4 + - - +
81A PHE* 4.0 11.9 - - + -
82A LEU* 3.9 5.5 - - - +
91A ARG 2.7 23.8 + - - -
92A GLY 4.1 0.7 - - - -
94A VAL* 1.3 76.4 - - - +
96A ARG* 1.3 56.0 + - - +
97A ALA 3.2 2.5 - - - -
98A LYS* 2.7 28.9 + - - -
99A LEU* 2.9 21.3 + - + -
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Residues in contact with ARG 96 (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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65A VAL* 5.3 3.1 - - + +
92A GLY 3.0 18.4 + - - +
93A ASP 3.8 8.6 + - - +
95A THR* 1.3 75.2 - - - +
97A ALA* 1.3 84.8 + - - +
99A LEU* 3.4 5.2 + - - +
100A ALA* 2.8 52.1 + - - +
108A VAL* 2.7 39.8 + - + +
109A ASN* 3.9 7.6 - - - +
110A VAL* 3.5 31.0 - - + +
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Residues in contact with ALA 97 (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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93A ASP 4.2 6.0 + - - +
94A VAL 4.8 6.5 - - - +
95A THR 3.1 1.2 + - - -
96A ARG* 1.3 97.8 - - - +
98A LYS* 1.3 63.0 + - + +
100A ALA* 3.4 5.1 + - - +
101A GLU* 3.4 31.7 + - - +
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Residues in contact with LYS 98 (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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80A PHE 5.7 0.2 + - - -
81A PHE* 3.6 66.0 + - + +
83A THR* 4.1 20.2 - - - +
86A ASP* 5.1 2.0 + - - -
94A VAL* 3.7 18.6 - - - +
95A THR 2.7 13.5 + - - +
97A ALA* 1.3 72.5 - - + +
99A LEU* 1.3 62.8 + - - +
101A GLU* 3.3 30.9 + - - +
102A LEU* 4.0 3.8 + - - +
486A ARG* 4.7 1.9 + - - -
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Residues in contact with LEU 99 (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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44A LEU* 3.8 16.6 - - + -
49A VAL* 4.3 4.3 - - + -
52A ALA* 3.8 31.9 - - + +
53A LYS* 3.9 12.1 - - - +
56A VAL* 3.9 12.7 - - + +
63A MET* 5.0 2.2 - - + -
65A VAL* 4.1 12.1 - - + -
81A PHE* 3.9 18.1 - - + -
95A THR* 2.9 33.4 + - + +
96A ARG 3.7 6.7 - - - +
98A LYS* 1.3 72.7 - - - +
100A ALA* 1.3 56.8 + - - +
101A GLU 3.0 4.0 - - - -
102A LEU* 3.0 38.7 + - + +
108A VAL* 4.0 17.0 - - + -
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Residues in contact with ALA 100 (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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96A ARG* 2.8 43.3 + - - +
97A ALA* 3.5 7.2 - - - +
98A LYS 3.3 0.4 - - - -
99A LEU* 1.3 73.1 - - - +
101A GLU* 1.3 59.0 + - - +
102A LEU 3.3 0.4 + - - -
103A ASN 4.4 11.9 + - - +
104A ALA* 5.0 3.6 + - - -
106A VAL 5.0 2.9 - - - +
108A VAL* 3.8 21.9 - - + +
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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