Contacts of the helix formed by residues 96 - 107 (chain C) in PDB entry 4CQM
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 96 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94C ARG 5.3 3.4 - - - +
95C THR* 1.3 76.0 - - - +
97C THR* 1.3 65.1 + - - +
98C GLU* 3.3 5.6 - - + +
99C ASP* 3.3 37.0 + - - +
100C MET* 3.5 12.2 + - - +
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Residues in contact with THR 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B GLU* 2.8 47.3 + - + +
109B LEU* 4.3 13.2 - - + -
113B LEU* 3.9 21.3 - - + +
116B LYS* 5.7 4.7 + - - +
95C THR 3.8 1.0 + - - -
96C LYS* 1.3 74.1 - - - +
98C GLU* 1.3 68.6 + - - +
99C ASP 3.1 0.2 - - - -
100C MET* 3.0 14.5 + - - +
101C VAL* 3.0 27.2 + - + +
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Residues in contact with GLU 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B GLU* 5.0 9.1 - - - +
96C LYS* 3.3 3.8 - - + +
97C THR* 1.3 84.7 - - - +
99C ASP* 1.3 61.9 + - - +
101C VAL* 3.7 32.2 - - - +
102C SER* 3.2 23.7 + - - -
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Residues in contact with ASP 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C ARG* 5.3 17.4 + - + -
95C THR* 5.6 5.2 - - + -
96C LYS* 3.3 42.9 + - + +
97C THR 3.1 0.6 - - - -
98C GLU* 1.3 79.8 - - - +
100C MET* 1.3 64.0 + - + +
101C VAL 3.3 0.7 - - - -
102C SER* 3.9 6.1 - - - -
103C GLN* 3.3 41.1 + - - +
147C VAL* 4.9 0.2 - - - -
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Residues in contact with MET 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B LEU* 4.0 15.6 - - + +
112B MET* 3.6 42.9 - - + +
113B LEU* 4.0 24.0 - - + -
116B LYS* 4.9 6.7 - - - -
92C LEU* 4.5 7.4 - - + -
95C THR* 4.2 19.7 - - - +
96C LYS 3.6 15.9 - - - +
97C THR* 3.0 14.1 + - - +
99C ASP* 1.3 77.8 - - - +
101C VAL* 1.3 58.9 + - - +
104C LEU* 3.2 28.1 + - - +
147C VAL* 3.7 35.2 - - + +
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Residues in contact with VAL 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B HIS* 4.2 13.0 - - + -
109B LEU* 3.9 24.0 - - + -
97C THR* 3.0 24.5 + - + +
98C GLU* 3.7 31.4 - - - +
99C ASP 3.3 0.2 - - - -
100C MET* 1.3 76.5 - - - +
102C SER* 1.3 64.4 + - - +
104C LEU* 3.2 2.6 + - - -
105C HIS* 3.0 53.4 + - + +
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Residues in contact with SER 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C ALA* 5.4 0.2 - - - +
86C ILE* 3.5 17.2 - - - +
98C GLU 3.2 19.3 + - - -
99C ASP* 3.9 11.2 - - - -
100C MET 3.4 0.2 - - - -
101C VAL* 1.3 81.2 - - - +
103C GLN* 1.3 60.9 + - - +
105C HIS* 3.4 4.7 + - - +
106C THR* 3.1 28.9 + - - -
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Residues in contact with GLN 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C ILE* 3.6 40.6 - - + +
87C ASN* 4.1 2.8 - - - +
88C ARG* 4.0 30.7 + - - +
99C ASP* 3.3 26.2 + - + +
102C SER* 1.3 76.2 - - - +
104C LEU* 1.3 57.2 + - - +
107C ASN* 2.9 39.9 + - - +
147C VAL* 3.8 23.3 - - + +
148C TYR* 3.8 27.2 + - - +
151C SER* 3.6 5.1 - - - +
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Residues in contact with LEU 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B LEU* 4.0 21.1 - - + +
105B HIS* 5.6 1.6 - - + -
108B LEU* 3.6 40.4 - - + -
109B LEU* 3.7 31.4 - - + -
112B MET* 4.1 4.9 - - + -
100C MET 3.2 15.4 + - - +
101C VAL* 3.2 5.8 + - - +
102C SER 3.2 0.6 - - - -
103C GLN* 1.3 79.7 - - - +
105C HIS* 1.3 64.1 + - + +
108C LEU* 3.4 14.3 - - + +
109C LEU* 3.1 22.2 + - - +
147C VAL* 5.3 1.8 - - + +
150C ALA* 4.4 3.1 - - + -
151C SER* 3.7 26.0 - - - +
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Residues in contact with HIS 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B VAL* 4.0 16.0 - - + +
104B LEU* 4.8 6.0 - - + +
105B HIS* 2.9 34.6 + + - -
58C ALA* 3.6 26.5 + - + +
101C VAL* 3.0 34.4 + - + +
102C SER* 4.0 4.0 - - - +
103C GLN 3.2 0.2 - - - -
104C LEU* 1.3 86.1 - - + +
106C THR* 1.3 62.7 + - - +
109C LEU* 3.4 27.4 - - + +
110C GLY* 2.8 25.6 + - - -
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Residues in contact with THR 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C ARG* 6.5 0.2 - - - -
56C ASP* 4.9 2.4 + - - +
57C VAL* 3.7 29.9 - - + +
58C ALA* 4.1 11.0 - - - +
84C ALA* 3.7 8.6 - - + +
85C GLY* 4.1 15.7 - - - +
86C ILE* 3.9 21.2 - - + +
102C SER* 3.1 19.0 + - - -
105C HIS* 1.3 78.5 - - - +
107C ASN* 1.3 77.2 + - - +
108C LEU 3.4 0.6 + - - -
110C GLY* 3.7 8.0 - - - -
111C SER* 4.3 2.3 + - - -
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Residues in contact with ASN 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C ALA 4.1 6.5 - - - -
85C GLY* 3.3 7.6 - - - -
86C ILE* 2.9 45.5 + - - +
103C GLN* 2.9 21.9 + - - +
106C THR* 1.3 78.8 - - - +
108C LEU* 1.3 57.7 + - - +
111C SER* 3.6 7.4 + - - -
148C TYR* 3.2 26.7 - - - -
151C SER* 3.4 19.1 + - - +
152C LYS* 3.7 14.0 + - + +
155C LEU* 3.4 26.0 - - - +
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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