Contacts of the helix formed by residues 77 - 93 (chain C) in PDB entry 1CDL
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 77 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76C MET* 1.3 75.9 - - - +
78C ASP* 1.3 59.8 + - - +
79C THR* 3.1 5.8 - - - -
80C ASP* 2.7 35.2 + - - +
81C SER* 2.9 10.1 + - - -
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Residues in contact with ASP 78 (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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76C MET 3.7 2.4 + - - +
77C LYS* 1.3 71.1 - - - +
79C THR* 1.3 64.6 + - + +
81C SER* 3.5 9.0 + - - -
82C GLU* 3.1 24.8 + - - +
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Residues in contact with THR 79 (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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126A ARG* 3.3 40.3 + - - +
77C LYS* 4.5 2.9 + - - -
78C ASP* 1.3 78.9 - - + +
80C ASP* 1.3 70.5 + - - +
83C GLU* 3.3 17.0 + - - +
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Residues in contact with ASP 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C MET* 3.8 29.9 - - + +
77C LYS* 2.7 23.6 + - - +
79C THR* 1.3 78.8 + - - +
81C SER* 1.3 59.7 + - - +
83C GLU* 3.4 6.7 + - - +
84C GLU* 2.9 27.7 + - - +
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Residues in contact with SER 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C MET* 4.0 22.5 + - - +
77C LYS 2.9 11.8 + - - -
78C ASP* 3.8 11.4 - - - -
80C ASP* 1.3 73.0 - - - +
82C GLU* 1.3 66.6 + - - +
84C GLU* 2.9 25.6 + - - +
85C ILE* 3.0 17.9 + - - +
812G ARG* 5.7 0.9 + - - -
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Residues in contact with GLU 82 (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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126A ARG* 3.2 38.6 + - - +
134A GLY* 5.1 3.6 - - - -
78C ASP 3.1 18.1 + - - +
80C ASP 3.4 0.2 - - - -
81C SER* 1.3 74.0 - - - +
83C GLU* 1.3 51.2 + - - +
85C ILE* 3.0 9.1 + - - +
86C ARG* 2.7 56.2 + - - +
138C TYR* 3.4 25.2 + - - +
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Residues in contact with GLU 83 (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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119A GLU* 4.1 27.8 - - + +
122A ASP* 3.2 31.3 - - - +
126A ARG* 3.5 16.4 + - - +
79C THR 3.3 14.8 + - - +
80C ASP* 3.7 6.5 - - - +
81C SER 3.2 0.4 - - - -
82C GLU* 1.3 75.5 - - - +
84C GLU* 1.3 59.8 + - - +
86C ARG* 4.1 2.6 - - - +
87C GLU* 2.9 36.9 + - + +
90C ARG* 3.3 18.4 + - - -
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Residues in contact with GLU 84 (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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76C MET* 3.5 16.5 - - + +
80C ASP 2.9 14.8 + - - +
81C SER* 2.9 20.4 + - - +
83C GLU* 1.3 77.9 - - - +
85C ILE* 1.3 55.7 + - + +
87C GLU* 3.9 7.6 - - - +
88C ALA* 3.0 25.5 + - - +
808G ARG* 3.1 48.0 + - + +
811G GLY* 5.9 4.7 - - - -
812G ARG* 2.7 47.0 + - - +
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Residues in contact with ILE 85 (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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81C SER* 3.0 14.8 + - - +
82C GLU* 3.0 10.1 + - - +
84C GLU* 1.3 76.4 - - - +
86C ARG* 1.3 54.7 + - - +
87C GLU 3.1 1.3 - - - -
88C ALA* 2.9 5.3 + - + +
89C PHE* 2.6 34.3 + - - +
138C TYR* 3.9 15.5 - - + +
141C PHE* 3.4 27.6 - - + -
142C VAL* 3.9 22.2 - - + +
145C MET* 4.1 22.9 - - + +
146C THR* 5.0 7.0 - - + -
808G ARG* 4.6 15.5 - - - -
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Residues in contact with ARG 86 (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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101A SER* 6.0 0.2 - - - -
102A ALA* 3.5 26.6 - - - +
122A ASP* 3.3 36.9 + - - +
125A ILE* 3.3 23.0 - - - +
126A ARG* 4.6 3.2 - - - +
134A GLY* 2.7 39.3 + - - -
82C GLU* 2.7 36.6 + - - +
83C GLU* 3.8 9.4 - - - +
85C ILE* 1.3 71.5 - - - +
87C GLU* 1.3 57.7 + - - +
89C PHE* 3.2 5.5 + - - +
90C ARG* 3.0 33.9 + - - +
138C TYR* 3.6 45.1 - - - +
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Residues in contact with GLU 87 (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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41C GLN* 5.0 10.0 + - - +
83C GLU* 2.9 22.0 + - - +
84C GLU* 3.9 7.2 - - - +
86C ARG* 1.3 76.5 - - - +
88C ALA* 1.3 65.8 + - - +
90C ARG* 3.1 38.9 + - + +
91C VAL* 3.1 20.6 + - + +
811G GLY* 3.9 26.5 - - - +
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Residues in contact with ALA 88 (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 GLU 3.0 16.3 + - - +
85C ILE* 2.9 12.2 + - + +
87C GLU* 1.3 77.3 - - - +
89C PHE* 1.3 63.5 + - - +
91C VAL* 3.4 6.2 + - - +
92C PHE* 3.0 23.2 + - - -
141C PHE* 3.8 17.5 - - + -
145C MET* 6.0 1.1 - - + -
804G GLY* 5.4 0.7 - - - +
807G VAL* 3.9 25.1 - - + -
808G ARG* 4.4 15.3 - - + +
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Residues in contact with PHE 89 (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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85C ILE 2.6 16.0 + - - +
86C ARG 3.4 9.2 - - - +
88C ALA* 1.3 74.3 - - - +
90C ARG* 1.3 68.4 + - + +
92C PHE* 3.2 6.7 + - - +
93C ASP* 3.0 31.2 + - + -
98C GLY* 3.3 36.1 - - - -
99C TYR 4.3 0.2 - - - -
100C ILE* 3.3 33.4 - - + -
136C VAL 3.7 0.9 - - - -
137C ASN 3.3 23.1 - - - -
138C TYR* 3.4 34.5 - + + -
141C PHE* 3.6 28.6 - + + -
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Residues in contact with ARG 90 (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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106A ARG* 3.7 31.4 - - - +
118A ASP* 3.5 34.5 + - - +
119A GLU* 4.3 5.1 + - - -
122A ASP* 2.8 29.6 + - - -
83C GLU* 3.3 13.5 + - - -
86C ARG* 3.0 21.9 + - - +
87C GLU* 3.1 41.0 + - + +
89C PHE* 1.3 83.0 - - + +
91C VAL* 1.3 64.4 + - - +
93C ASP* 3.0 23.9 - - - +
94C LYS* 3.9 8.2 - - - +
96C GLY* 6.3 2.2 - - - -
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Residues in contact with VAL 91 (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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39C LEU* 4.0 37.5 - - + +
41C GLN* 3.8 21.3 - - - +
87C GLU* 3.1 20.2 + - + +
88C ALA* 3.8 6.5 - - - +
89C PHE 3.2 0.6 - - - -
90C ARG* 1.3 78.1 - - + +
92C PHE* 1.3 65.1 + - - +
94C LYS* 3.2 31.4 - - - +
108C VAL* 4.6 9.8 - - + +
807G VAL* 4.1 21.5 - - + -
810G ILE* 5.9 2.0 - - + -
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Residues in contact with PHE 92 (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 ALA 3.0 24.2 - - - -
89C PHE 3.2 3.0 + - - +
91C VAL* 1.3 79.0 - - + +
93C ASP* 1.3 58.8 + - - +
94C LYS* 3.1 7.8 + - - +
100C ILE* 3.5 32.3 - - + +
104C GLU* 3.2 21.7 - - - +
105C LEU* 3.6 30.1 - - + -
108C VAL* 3.7 32.5 - - + +
109C MET* 5.6 0.2 - - + -
141C PHE* 3.7 23.8 - + - -
145C MET* 5.4 0.2 - - + -
800G TRP* 4.5 7.9 - + - -
803G THR* 3.9 22.4 - - - -
804G GLY* 4.7 3.4 - - - -
807G VAL* 3.6 36.1 - - + -
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Residues in contact with ASP 93 (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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103A ALA* 5.1 0.3 - - - +
89C PHE* 3.0 27.7 + - + +
90C ARG* 3.0 14.5 - - - +
92C PHE* 1.3 74.7 - - - +
94C LYS* 1.3 61.0 + - - +
95C ASP* 2.6 8.3 - - - +
96C GLY* 3.2 10.6 + - - -
97C ASN* 2.9 5.2 + - - +
98C GLY* 2.6 32.7 + - - -
99C TYR 3.2 11.7 - - - +
100C ILE* 4.3 5.2 - - + -
104C GLU* 2.7 6.1 - - - +
150C CA 2.0 35.1 - - - -
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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