Contacts of the helix formed by residues 99 - 117 (chain C) in PDB entry 1CBM
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 ASP 99 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A TRP* 3.3 21.5 - - + +
40A ARG* 2.7 34.2 + - - -
99A ASP* 3.4 13.4 - - - +
101A GLU* 5.8 1.5 - - + +
102A ASN* 2.8 32.6 + - - +
41C PHE* 3.7 0.2 - - - -
97C HIS 3.8 0.3 - - - +
98C VAL* 1.3 78.6 - - - +
100C PRO* 1.3 70.2 - - + +
101C GLU* 4.3 9.0 - - + +
102C ASN* 2.8 35.0 + - - +
103C PHE* 3.9 1.6 + - - -
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Residues in contact with PRO 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A TRP* 3.5 45.3 - - + -
98C VAL 3.8 3.1 - - - +
99C ASP* 1.3 86.2 - - + +
101C GLU* 1.3 60.6 + - - +
103C PHE* 3.1 31.9 + - + +
104C ARG* 3.5 16.3 + - - +
142C ALA* 4.1 20.9 - - + -
145C TYR* 3.8 9.4 - - + -
146C HIS* 5.9 0.9 - - - +
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Residues in contact with GLU 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A ASP* 5.9 2.9 - - + +
101A GLU* 4.4 36.1 - - + +
99C ASP* 3.2 7.8 - - + -
100C PRO* 1.3 78.5 - - - +
102C ASN* 1.3 60.4 + - - +
104C ARG* 3.1 25.7 + - - +
105C LEU* 3.0 46.1 + - + +
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Residues in contact with ASN 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A ASP* 2.7 23.2 + - - +
31C LEU* 4.7 1.2 - - - +
37C TRP* 3.1 24.0 + - - +
38C THR* 3.6 15.2 - - + +
41C PHE* 3.8 16.2 - - - -
98C VAL* 3.9 4.0 - - + -
99C ASP* 2.8 30.5 + - - +
101C GLU* 1.3 78.9 - - - +
103C PHE* 1.3 62.0 + - - +
105C LEU* 3.4 12.4 + - - +
106C LEU* 3.1 18.7 + - - +
147C HEM 3.2 29.7 - - + +
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Residues in contact with PHE 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C HIS* 3.7 38.8 - + + -
93C CYS* 4.4 6.1 - - - -
98C VAL* 3.9 27.1 - - + -
99C ASP 4.5 0.2 - - - -
100C PRO* 3.1 28.6 + - + +
102C ASN* 1.3 76.1 - - - +
104C ARG* 1.3 62.7 - - - +
106C LEU 3.5 0.5 + - - -
107C GLY* 3.2 17.8 + - - -
134C VAL 5.3 0.2 - - - +
138C ALA* 3.8 37.2 - - + +
141C LEU* 3.8 20.9 - - + -
142C ALA* 3.7 24.7 - - + -
145C TYR* 4.4 0.7 - + - -
147C HEM 3.8 35.0 - + + +
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Residues in contact with ARG 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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100C PRO* 3.5 15.7 + - - +
101C GLU* 3.1 26.2 + - - +
103C PHE* 1.3 75.9 - - - +
105C LEU* 1.3 64.9 + - + +
107C GLY* 3.2 3.4 + - - -
108C ASN* 3.0 33.0 + - - +
134C VAL* 5.6 0.6 - - - +
135C ALA* 3.5 33.9 + - - +
138C ALA* 3.7 16.7 + - + +
139C ASN* 3.1 32.3 - - - +
142C ALA* 5.5 4.4 - - - +
146C HIS* 5.6 1.6 + - - -
104D ARG* 5.7 8.1 - - - +
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Residues in contact with LEU 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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31C LEU* 3.9 14.1 - - + -
35C TYR* 3.9 35.7 - - + +
37C TRP* 3.7 26.0 - - + +
101C GLU* 3.0 34.2 + - + +
102C ASN* 3.4 28.9 + - - +
104C ARG* 1.3 72.1 - - + +
106C LEU* 1.3 61.8 + - - +
108C ASN* 3.1 13.8 + - + +
109C VAL* 2.8 33.3 + - - +
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Residues in contact with LEU 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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27C ALA* 4.1 33.4 - - + +
28C LEU* 4.5 8.1 - - + +
31C LEU* 3.8 22.4 - - + +
67C VAL* 4.2 16.2 - - + -
71C PHE* 4.9 6.1 - - + -
102C ASN 3.1 16.5 + - - +
103C PHE 3.9 4.3 - - - +
104C ARG 3.3 0.2 - - - -
105C LEU* 1.3 76.0 - - - +
107C GLY* 1.3 57.2 + - - +
109C VAL* 3.2 2.5 + - + -
110C LEU* 2.9 28.6 + - + +
147C HEM 3.6 52.3 - - + -
148C CMO 4.8 3.8 - - - +
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Residues in contact with GLY 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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71C PHE* 4.9 7.4 - - - -
103C PHE 3.2 13.6 + - - -
104C ARG 3.2 4.6 + - - -
106C LEU* 1.3 75.0 - - - +
108C ASN* 1.3 61.2 + - - +
110C LEU* 3.2 7.7 + - - +
111C VAL* 3.0 26.7 + - - +
134C VAL* 3.6 32.8 - - - +
147C HEM 4.7 1.0 - - - +
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Residues in contact with ASN 108 (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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35B TYR* 5.0 2.7 + - - -
108B ASN* 5.2 11.5 - - + +
112B CYS* 5.0 3.1 - - - -
35C TYR* 5.6 4.3 - - - +
104C ARG* 3.0 28.5 + - - +
105C LEU* 3.6 18.0 - - + +
107C GLY* 1.3 73.0 - - - +
109C VAL* 1.3 67.9 + - + +
111C VAL* 3.3 8.9 + - - +
112C CYS* 3.2 20.6 + - - +
131C GLN* 3.4 27.6 + - - +
134C VAL* 4.6 1.7 - - - +
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Residues in contact with VAL 109 (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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127B GLN* 4.7 13.5 - - - +
27C ALA* 3.4 31.9 - - + +
30C ARG* 3.8 20.6 - - + -
31C LEU* 4.0 9.4 - - + +
34C VAL* 5.5 0.2 - - + -
35C TYR* 3.6 30.5 - - + +
105C LEU 2.8 21.1 + - - +
106C LEU* 3.7 7.2 - - + +
108C ASN* 1.3 77.4 - - + +
110C LEU* 1.3 65.3 + - - +
112C CYS* 3.2 7.4 + - - +
113C VAL* 2.9 23.2 + - + +
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Residues in contact with LEU 110 (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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15C TRP* 4.6 17.0 - - + -
23C VAL* 4.2 24.5 - - + -
24C GLY* 6.2 0.2 - - - -
27C ALA* 4.2 20.6 - - + +
68C LEU* 4.9 4.9 - - + -
71C PHE* 4.0 42.2 - - + -
106C LEU* 2.9 14.7 + - + +
107C GLY* 3.4 8.7 - - - +
109C VAL* 1.3 76.6 - - - +
111C VAL* 1.3 58.6 - - - +
113C VAL* 3.1 4.6 + - + +
114C LEU* 2.9 42.3 + - + +
130C TYR* 5.8 1.1 - - + -
134C VAL* 4.2 11.7 - - + -
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Residues in contact with VAL 111 (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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112B CYS* 4.2 13.2 - - - -
107C GLY 3.0 16.4 + - - +
108C ASN* 3.7 10.1 - - - +
109C VAL 3.2 0.2 - - - -
110C LEU* 1.3 77.4 - - - +
112C CYS* 1.3 61.4 + - - +
114C LEU* 3.3 9.7 + - + +
115C ALA* 3.0 21.7 + - - +
122C PHE* 3.9 20.7 - - + -
127C GLN* 4.2 15.3 - - + +
130C TYR* 4.2 22.2 - - + +
131C GLN* 4.4 12.3 - - - +
134C VAL* 4.0 25.6 - - + -
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Residues in contact with CYS 112 (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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111B VAL* 4.3 7.2 - - - -
112B CYS* 3.9 25.3 - - - -
115B ALA* 3.7 22.5 - - - +
122B PHE* 4.1 9.4 - - - -
127B GLN* 3.9 28.0 - - - +
30C ARG* 5.9 0.2 - - - -
108C ASN 3.2 12.4 + - - +
109C VAL* 3.4 10.1 - - + +
111C VAL* 1.3 76.8 - - - +
113C VAL* 1.3 60.8 + - + +
115C ALA* 3.3 3.9 + - - +
116C HIS* 2.9 28.2 + - - +
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Residues in contact with VAL 113 (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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23C VAL* 4.0 28.9 - - + +
26C GLU* 3.7 26.5 - - + +
27C ALA* 4.0 15.5 - - + -
30C ARG* 3.8 28.7 - - - +
109C VAL* 2.9 18.1 + - + +
110C LEU* 3.1 9.4 + - - +
112C CYS* 1.3 74.8 - - + +
114C LEU* 1.3 65.1 + - - +
116C HIS* 3.3 6.0 + - - -
117C HIS* 3.0 40.1 + - + +
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Residues in contact with LEU 114 (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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14C LEU* 4.5 3.1 - - + -
15C TRP* 4.4 10.5 - - + -
18C VAL* 4.2 25.4 - - + -
23C VAL* 4.4 18.6 - - + -
110C LEU* 2.9 26.1 + - + +
111C VAL* 3.3 11.0 + - - +
113C VAL* 1.3 73.6 - - - +
115C ALA* 1.3 62.1 - - - +
117C HIS* 3.3 1.5 + - + -
118C PHE* 2.8 50.7 + - + +
122C PHE* 3.8 16.2 - - + -
130C TYR* 3.7 44.2 - - + -
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Residues in contact with ALA 115 (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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112B CYS* 3.6 27.4 - - + +
116B HIS* 3.3 18.6 - - + +
111C VAL 3.0 11.8 + - - +
112C CYS* 3.6 9.9 - - - +
113C VAL 3.2 0.2 - - - -
114C LEU* 1.3 77.3 - - - +
116C HIS* 1.3 58.4 + - - +
119C GLY* 2.9 25.8 + - - -
122C PHE* 3.6 30.9 - - + -
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Residues in contact with HIS 116 (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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115B ALA* 3.3 16.7 - - + +
116B HIS 5.5 0.2 - - - +
119B GLY* 2.8 53.2 + - - -
120B LYS* 3.8 8.2 + - + -
122B PHE* 3.2 32.5 + + + -
26C GLU* 3.7 8.9 + - - -
30C ARG* 3.5 17.9 + - - -
112C CYS 2.9 17.1 + - - +
113C VAL* 3.5 6.5 - - - +
115C ALA* 1.3 79.8 - - - +
117C HIS* 1.3 84.9 + + - +
119C GLY* 4.3 2.9 + - - -
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Residues in contact with HIS 117 (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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22C GLU* 3.5 25.3 + - + -
23C VAL* 3.4 30.3 - - + +
26C GLU* 4.1 14.1 + - + +
113C VAL* 3.0 26.1 + - + +
114C LEU* 3.9 4.0 - - + +
115C ALA 3.3 0.2 - - - -
116C HIS* 1.3 105.6 + + - +
118C PHE* 1.3 77.7 + - + +
119C GLY 3.5 0.2 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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