Contacts of the helix formed by residues 101 - 109 (chain A) in PDB entry 1SMB
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 THR 101 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86A GLU* 3.1 34.5 - - - +
89A ASN* 3.6 29.4 - - + +
90A TYR* 3.7 26.7 - - + +
98A THR* 2.6 31.0 + - + +
99A SER 3.2 0.6 - - - -
100A GLY* 1.3 79.6 - - - +
102A GLY* 1.3 57.2 + - - +
104A PHE* 3.2 6.2 + - - +
105A THR* 2.9 30.5 + - - +
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Residues in contact with GLY 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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66A ASN* 4.2 0.5 - - - +
86A GLU* 3.5 0.2 + - - -
97A PHE* 4.5 7.2 - - - -
98A THR 3.2 12.3 + - - -
99A SER 3.2 10.2 + - - -
101A THR* 1.3 77.7 - - - +
103A HIS* 1.3 63.6 + - - +
105A THR* 3.6 8.1 - - - -
106A ALA* 3.2 14.4 + - - +
138A ASN* 3.1 24.0 - - - +
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Residues in contact with HIS 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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54A HIS* 5.4 7.4 + + - -
65A GLU 4.8 2.2 + - - -
66A ASN* 3.1 45.7 + - + +
67A LEU* 4.2 19.6 + - - +
83A TRP* 3.8 29.6 - + + -
86A GLU* 2.9 27.8 + - - +
99A SER 4.9 0.4 + - - -
102A GLY* 1.3 75.7 - - - +
104A PHE* 1.3 65.0 + - - +
106A ALA 3.5 0.7 + - - -
107A MET* 3.1 22.0 + - - +
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Residues in contact with PHE 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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24A HIS* 3.8 11.4 - + - -
83A TRP 3.5 18.3 + - - +
84A TYR* 3.6 44.2 - + - +
86A GLU* 3.1 17.5 + - + -
87A ILE* 3.5 38.4 - - + -
90A TYR* 4.0 19.3 - + + -
92A PHE* 4.0 5.4 - + - -
101A THR* 3.2 7.2 + - - +
103A HIS* 1.3 77.1 - - - +
105A THR* 1.3 80.8 + - + +
107A MET* 3.1 14.5 + - - +
108A VAL* 3.2 28.2 + - + +
149A VAL* 4.0 10.1 - - + -
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Residues in contact with THR 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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90A TYR* 3.8 28.5 - - + -
97A PHE* 5.0 0.9 - - - -
101A THR* 2.9 21.7 + - - +
102A GLY* 3.5 6.8 + - - -
104A PHE* 1.3 91.2 - - + +
106A ALA* 1.3 62.5 + - - +
108A VAL* 3.9 5.8 - - - +
109A TRP* 3.1 28.6 + - - +
138A ASN* 2.6 28.2 + - - -
145A PHE* 3.8 15.7 - - + -
149A VAL* 3.9 11.8 - - + +
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Residues in contact with ALA 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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21A ARG* 4.7 1.4 + - - -
64A GLY* 6.0 2.0 - - - -
65A GLU 5.6 2.2 - - - +
66A ASN* 3.9 15.9 - - - +
102A GLY 3.2 19.9 + - - +
103A HIS 3.8 4.0 - - - +
104A PHE 3.2 0.2 - - - -
105A THR* 1.3 77.1 + - - +
107A MET* 1.3 63.6 + - - +
108A VAL 3.5 0.2 + - - -
109A TRP* 3.5 16.4 + - - +
112A THR* 4.5 4.0 + - - -
133A TYR* 4.3 26.6 - - + +
137A GLY* 5.5 4.4 - - - +
138A ASN* 3.6 15.5 - - - +
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Residues in contact with MET 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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17A HIS* 3.7 50.8 - - + +
20A TYR* 3.9 25.6 - - + -
21A ARG* 2.9 28.2 + - - +
29A LEU* 4.4 2.3 - - - +
66A ASN* 3.8 9.2 - - - +
80A ALA* 3.6 17.9 - - + +
83A TRP* 3.5 12.1 - - + -
84A TYR* 3.5 33.4 - - + -
103A HIS 3.1 16.8 + - - +
104A PHE* 3.1 7.2 + - - +
106A ALA* 1.3 77.3 - - - +
108A VAL* 1.3 63.5 - - + +
133A TYR* 4.5 3.1 - - - -
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Residues in contact with VAL 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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20A TYR* 4.5 8.3 - - + +
21A ARG* 3.4 15.7 - - + +
24A HIS* 3.9 35.2 - - + +
26A VAL* 3.7 14.1 - - + +
84A TYR* 4.1 11.9 - - + -
104A PHE* 3.2 41.3 + - + +
105A THR* 4.1 6.7 - - - +
107A MET* 1.3 78.6 - - + +
109A TRP* 1.3 64.7 + - - +
110A LYS 3.0 4.2 + - - -
148A ASN 3.4 5.7 - - - +
149A VAL* 4.3 14.6 - - + -
150A LEU 5.4 0.8 + - - +
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Residues in contact with TRP 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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21A ARG* 2.9 17.7 + - - -
105A THR 3.1 23.1 + - - +
106A ALA 3.5 8.3 + - - +
107A MET 3.4 2.6 - - - -
108A VAL* 1.3 72.9 - - - +
110A LYS* 1.3 67.1 + - - +
111A ASN* 3.8 11.3 - - - +
112A THR* 3.1 40.1 + - - +
135A PRO 5.1 0.4 - - - -
136A ALA 4.4 3.9 + - - -
137A GLY* 3.6 17.4 - - - -
138A ASN* 3.5 20.2 - - - -
139A VAL* 3.4 47.1 - - + +
144A PHE* 3.8 11.7 - + + -
145A PHE* 3.8 17.3 - + - -
148A ASN* 3.4 33.3 + - + +
149A VAL* 3.7 25.6 - - + -
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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