Contacts of the helix formed by residues 99 - 117 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A ARG* 2.8 21.5 + - - -
97A HIS 3.9 3.6 - - - +
98A VAL* 1.3 76.2 - - - +
100A PRO* 1.3 66.2 - - + +
101A GLU* 4.1 10.8 - - + +
102A ASN* 2.8 39.3 + - - +
103A PHE* 3.8 0.9 + - - -
37C TRP* 3.2 25.2 - - + +
41C PHE* 4.8 0.3 - - - -
99C ASP* 3.4 16.2 - - + +
101C GLU* 5.9 3.2 - - + +
102C ASN* 2.7 34.2 + - - +
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Residues in contact with PRO 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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98A VAL 3.4 3.8 - - - +
99A ASP* 1.3 86.2 - - + +
101A GLU* 1.3 62.7 + - - +
102A ASN 3.1 0.7 + - - -
103A PHE* 3.1 31.8 + - + +
104A ARG* 3.6 12.9 + - - -
138A ALA* 5.4 0.2 - - - +
142A ALA* 4.1 15.5 - - + -
145A TYR* 3.6 14.1 - - + -
146A HIS* 6.0 0.9 - - - +
37C TRP* 3.6 45.3 - - + -
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Residues in contact with GLU 101 (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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99A ASP* 3.1 8.2 - - + -
100A PRO* 1.3 79.0 - - - +
102A ASN* 1.3 64.8 + - - +
104A ARG* 2.8 49.5 + - - +
105A LEU* 3.0 43.4 + - + +
99C ASP* 5.8 1.6 - - + +
101C GLU* 4.4 35.7 - - + -
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Residues in contact with ASN 102 (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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31A LEU* 4.5 1.4 - - - +
37A TRP* 3.2 24.0 + - - -
38A THR* 3.6 15.1 - - + +
41A PHE* 3.8 22.6 - - - -
98A VAL* 3.9 4.3 - - + -
99A ASP* 2.8 29.2 + - - +
101A GLU* 1.3 73.9 - - - +
103A PHE* 1.4 57.6 + - - +
105A LEU* 3.3 12.6 + - - +
106A LEU* 2.9 24.3 + - - +
147A HEM 3.3 27.9 - - + +
99C ASP* 2.8 23.0 + - - +
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Residues in contact with PHE 103 (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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92A HIS* 3.8 37.0 - + + -
93A CYS* 4.4 3.6 - - - -
98A VAL* 3.7 30.7 - - + -
99A ASP 4.6 0.2 - - - -
100A PRO* 3.1 27.8 + - + +
102A ASN* 1.4 79.2 - - - +
104A ARG* 1.3 61.8 + - - +
106A LEU* 3.4 3.6 + - - +
107A GLY* 3.2 18.5 + - - -
138A ALA* 3.8 35.5 - - + +
141A LEU* 3.8 14.8 - - + -
142A ALA* 3.8 25.1 - - + -
145A TYR* 4.4 3.4 - + - -
147A HEM 3.9 37.8 - - + +
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Residues in contact with ARG 104 (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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100A PRO* 3.6 17.9 + - - -
101A GLU* 2.8 48.6 + - - +
103A PHE* 1.3 76.2 - - - +
105A LEU* 1.3 66.2 + - + +
107A GLY* 3.2 4.1 + - - +
108A ASN* 3.0 31.0 + - - +
134A VAL* 5.6 0.2 - - - +
135A ALA* 6.1 2.5 - - - -
138A ALA* 4.1 17.0 - - + -
101B GLU* 5.2 0.6 + - - -
104B ARG* 4.0 29.5 - - - +
101D GLU* 5.4 4.9 + - - -
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Residues in contact with LEU 105 (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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31A LEU* 3.9 12.6 - - + -
35A TYR* 3.8 36.0 - - + +
37A TRP* 3.6 30.7 - - + +
38A THR* 5.1 0.2 - - + -
101A GLU* 3.0 35.2 + - + +
102A ASN* 3.3 24.2 + - - +
104A ARG* 1.3 77.1 - - - +
106A LEU* 1.3 61.5 + - - +
108A ASN* 3.3 15.2 + - - +
109A VAL* 3.0 26.0 + - - +
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Residues in contact with LEU 106 (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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27A ALA* 4.1 29.6 - - + +
28A LEU* 4.5 12.8 - - + +
31A LEU* 3.7 23.9 - - + +
67A VAL* 4.0 15.9 - - + -
71A PHE* 4.9 6.3 - - + -
102A ASN 2.9 17.2 + - - +
103A PHE 3.8 4.9 - - - +
104A ARG 3.3 0.2 - - - -
105A LEU* 1.3 75.2 - - - +
107A GLY* 1.3 52.7 - - - +
109A VAL* 3.2 2.3 + - + -
110A LEU* 2.9 33.3 + - + +
147A HEM 3.5 53.6 - - + -
148A CMO 4.9 0.4 - - - +
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Residues in contact with GLY 107 (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 PHE* 5.0 7.3 - - - -
103A PHE 3.2 13.1 + - - -
104A ARG* 3.2 5.1 + - - -
105A LEU 3.2 0.4 - - - -
106A LEU* 1.3 77.2 - - - +
108A ASN* 1.3 61.7 + - - +
110A LEU* 3.2 7.3 + - - +
111A VAL* 3.1 25.5 + - - +
134A VAL* 3.7 32.3 - - - +
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Residues in contact with ASN 108 (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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35A TYR* 5.0 10.1 + - - +
104A ARG* 3.0 20.3 + - - +
105A LEU* 3.5 21.0 - - - +
106A LEU 3.3 0.2 - - - -
107A GLY* 1.3 76.3 - - - +
109A VAL* 1.3 62.8 + - + +
111A VAL* 3.3 7.7 + - - +
112A CYS* 3.1 25.8 + - - +
131A GLN* 3.8 24.9 + - - +
134A VAL* 4.4 1.4 - - - +
35D TYR* 5.0 2.7 + - - -
108D ASN* 4.1 24.6 - - + +
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Residues in contact with VAL 109 (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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27A ALA* 3.3 33.9 - - + +
30A ARG* 3.7 21.1 - - + +
31A LEU* 3.9 15.7 - - + +
34A VAL* 5.3 0.2 - - + -
35A TYR* 3.6 27.4 - - + +
105A LEU 3.0 18.4 + - - +
106A LEU* 3.7 8.1 - - + +
108A ASN* 1.3 75.6 - - - +
110A LEU* 1.3 58.7 + - - +
112A CYS* 3.1 9.5 + - - +
113A VAL* 2.9 29.7 + - + +
127D GLN* 4.6 11.4 - - - +
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Residues in contact with LEU 110 (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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15A TRP* 4.6 14.6 - - + -
23A VAL* 4.1 12.6 - - + -
27A ALA* 3.9 24.2 - - + +
68A LEU* 4.1 18.8 - - + -
71A PHE* 4.0 40.6 - - + -
106A LEU* 2.9 14.5 + - + +
107A GLY* 3.2 11.0 + - - +
109A VAL* 1.3 77.4 - - - +
111A VAL* 1.3 61.7 + - - +
113A VAL* 3.1 6.7 + - + +
114A LEU* 3.0 35.1 + - + +
130A TYR* 5.9 1.3 - - + -
134A VAL* 4.3 10.1 - - + -
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Residues in contact with VAL 111 (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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107A GLY 3.1 14.8 + - - +
108A ASN* 3.3 8.9 + - - +
110A LEU* 1.3 73.9 - - - +
112A CYS* 1.3 57.7 + - - +
114A LEU* 3.3 10.4 + - + +
115A ALA* 3.0 27.0 + - - +
122A PHE* 3.9 21.5 - - + -
127A GLN* 4.2 13.0 - - + +
130A TYR* 4.2 20.2 - - + -
131A GLN* 4.2 17.3 - - - +
134A VAL* 4.1 25.1 - - + -
112D CYS* 4.2 12.6 - - + -
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Residues in contact with CYS 112 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A ARG* 6.2 0.2 - - - -
108A ASN* 3.1 16.0 + - - +
109A VAL 3.3 9.6 - - - +
111A VAL* 1.3 78.3 - - - +
113A VAL* 1.3 61.7 + - + +
115A ALA* 3.4 5.0 + - - +
116A HIS* 3.1 24.8 + - - +
108D ASN 4.9 2.7 - - - -
111D VAL* 4.0 17.5 - - - -
112D CYS* 3.8 32.8 - - - +
115D ALA* 3.6 10.7 - - + +
122D PHE* 5.5 0.4 - - + -
127D GLN* 4.1 20.4 - - - +
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Residues in contact with VAL 113 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A VAL* 3.7 31.9 - - + +
26A GLU* 3.7 26.2 - - - +
27A ALA* 3.9 19.7 - - + +
30A ARG* 3.7 30.3 - - - +
109A VAL* 2.9 17.4 + - + +
110A LEU* 3.1 10.1 + - - +
112A CYS* 1.3 73.4 - - - +
114A LEU* 1.3 62.5 + - + +
116A HIS* 3.3 9.0 - - - +
117A HIS* 3.0 27.7 + - + +
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Residues in contact with LEU 114 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A LEU* 4.4 3.6 - - + -
15A TRP* 4.4 10.1 - - + -
18A VAL* 3.8 29.2 - - + -
23A VAL* 4.7 13.0 - - + -
110A LEU* 3.0 30.0 + - + +
111A VAL* 3.6 12.3 - - + +
112A CYS 3.3 0.2 - - - -
113A VAL* 1.3 74.7 - - - +
115A ALA* 1.3 66.8 + - - +
117A HIS* 3.0 3.1 + - + -
118A PHE* 2.7 39.9 + - + +
122A PHE* 4.0 17.9 - - + -
130A TYR* 3.9 40.2 - - + -
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Residues in contact with ALA 115 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111A VAL 3.0 7.4 + - - +
112A CYS 3.7 7.2 - - - +
113A VAL 3.4 0.2 - - - -
114A LEU* 1.3 76.2 - - - +
116A HIS* 1.3 56.8 + - - +
119A GLY* 3.1 31.2 + - - +
122A PHE* 3.5 21.8 - - + -
112D CYS* 3.4 46.7 - - - +
116D HIS* 3.7 12.9 - - + +
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Residues in contact with HIS 116 (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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26A GLU* 3.2 19.6 + - - -
30A ARG* 3.9 11.0 + - - -
112A CYS 3.1 16.4 + - - +
113A VAL* 3.3 6.1 - - - +
115A ALA* 1.3 78.2 - - - +
117A HIS* 1.3 85.9 + + - +
119A GLY* 4.7 1.4 + - - -
115D ALA* 3.5 21.6 - - + +
119D GLY* 2.7 52.6 + - - -
120D LYS* 3.9 6.7 + - - -
122D PHE* 3.6 23.6 + + + -
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Residues in contact with HIS 117 (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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22A GLU* 3.7 19.5 + - - -
23A VAL* 3.5 29.6 - - + +
26A GLU* 2.7 34.0 + - - -
113A VAL* 3.0 18.1 + - + +
114A LEU* 3.7 4.3 - - + +
116A HIS* 1.3 111.9 + + - +
118A PHE* 1.3 76.6 + - + +
119A GLY 3.4 2.8 + - - -
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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