Contacts of the helix formed by residues 102 - 114 (chain A) in PDB entry 3SMZ
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 ASN 102 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A ASN* 5.0 3.4 - - - +
59A ARG* 3.8 16.7 - - - +
100A LEU* 3.4 3.3 - - - +
101A LEU* 1.3 98.9 - - + +
103A GLY* 1.3 63.1 + - - +
104A GLU* 3.2 14.8 + - - +
105A GLN* 3.1 32.2 + - - +
106A ALA* 3.3 20.6 + - - +
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Residues in contact with GLY 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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56A ARG* 3.3 28.4 + - - +
57A ASN* 4.6 4.8 + - - +
58A ARG 3.4 17.0 - - - +
59A ARG* 4.1 4.2 - - - +
102A ASN* 1.3 72.2 - - - +
104A GLU* 1.4 58.2 + - - +
106A ALA* 3.4 2.3 + - - +
107A GLU* 2.9 30.7 + - - +
127A LEU* 5.7 0.2 - - - +
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Residues in contact with GLU 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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56A ARG* 6.0 0.8 - - - +
102A ASN* 3.2 12.8 + - - +
103A GLY* 1.4 75.3 - - - +
105A GLN* 1.3 61.1 + - + +
107A GLU* 3.3 12.0 + - - +
108A ALA* 2.9 29.4 + - + +
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Residues in contact with GLN 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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81A ASP 4.2 5.4 + - - +
82A TYR* 3.4 26.3 - - + +
83A GLU* 3.8 27.1 + - - +
100A LEU* 3.9 12.3 - - + -
101A LEU* 4.3 15.9 - - + +
102A ASN* 3.1 29.0 + - - +
104A GLU* 1.3 77.2 - - + +
106A ALA* 1.4 60.5 + - - +
108A ALA* 3.3 6.0 + - - +
109A ALA* 2.9 31.4 + - - +
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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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58A ARG 3.4 26.0 - - - +
59A ARG 4.0 11.2 - - - +
61A ILE* 3.9 18.0 - - + +
100A LEU* 3.9 13.4 - - + +
102A ASN 3.3 11.1 + - - +
103A GLY 3.5 3.1 - - - +
104A GLU 3.3 0.2 - - - -
105A GLN* 1.4 78.0 - - - +
107A GLU* 1.3 61.0 + - - +
109A ALA* 3.4 2.1 + - - +
110A ILE* 3.1 30.3 + - - +
127A LEU* 4.2 2.7 - - + -
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Residues in contact with GLU 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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56A ARG* 4.8 19.1 + - - -
103A GLY 2.9 17.0 + - - +
104A GLU* 3.6 9.7 - - - +
106A ALA* 1.3 74.2 - - - +
108A ALA* 1.3 61.8 + - - +
110A ILE* 3.4 12.6 + - + +
111A ASN* 3.1 44.6 + - - +
127A LEU* 5.3 1.7 - - + +
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Residues in contact with ALA 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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82A TYR* 3.4 21.4 + - + +
104A GLU* 2.9 19.0 + - + +
105A GLN* 3.3 7.6 + - - +
107A GLU* 1.3 76.4 - - - +
109A ALA* 1.3 55.4 + - - +
111A ASN* 3.3 8.6 + - - +
112A ALA* 2.9 30.5 + - - +
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Residues in contact with ALA 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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61A ILE* 4.2 14.6 - - + -
79A LEU* 4.5 6.7 - - + -
82A TYR* 3.5 21.7 + - + -
100A LEU* 3.9 18.6 - - + -
105A GLN 2.9 17.7 + - - +
106A ALA 3.4 5.4 + - - +
108A ALA* 1.3 73.5 - - - +
110A ILE* 1.4 57.7 + - - +
113A PHE* 2.9 36.9 + - - +
125A VAL* 4.5 3.1 - - - +
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Residues in contact with ILE 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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61A ILE* 3.9 11.7 - - + -
106A ALA 3.1 21.7 + - - +
107A GLU* 3.6 11.7 - - + +
108A ALA 3.3 0.2 - - - -
109A ALA* 1.4 73.7 - - - +
111A ASN* 1.4 67.1 + - - +
114A HIS* 2.8 41.3 + - + +
125A VAL* 3.6 31.9 - - + +
126A GLN* 3.7 4.9 - - - -
127A LEU* 3.5 47.6 - - + +
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Residues in contact with ASN 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 GLU* 3.1 39.5 + - - +
108A ALA* 3.8 6.5 - - - +
110A ILE* 1.4 82.4 - - - +
112A ALA* 1.3 61.0 + - - +
114A HIS* 4.6 6.0 + - - +
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Residues in contact with ALA 112 (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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82A TYR* 4.0 9.0 - - - +
108A ALA 2.9 16.8 + - - +
110A ILE 3.2 0.2 - - - -
111A ASN* 1.3 78.5 - - - +
113A PHE* 1.4 87.1 + - + +
114A HIS 4.9 1.1 - - - +
116A SER* 4.1 9.0 - - - -
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Residues in contact with PHE 113 (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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63A ILE* 6.3 0.4 - - + -
78A LEU* 3.2 51.1 - - + -
79A LEU* 3.6 28.9 - - + -
81A ASP* 5.6 6.1 - - + -
82A TYR* 3.9 16.8 - + - -
109A ALA 2.9 25.2 + - - +
112A ALA* 1.4 92.9 - - + +
114A HIS* 1.3 63.0 + - - +
115A GLN 3.2 0.7 + - - -
116A SER* 2.7 38.5 + - - +
123A LEU* 4.1 5.6 - - + +
125A VAL* 3.6 21.4 - - + +
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Residues in contact with HIS 114 (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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110A ILE* 2.8 29.6 + - + +
111A ASN* 4.7 6.8 - - - +
112A ALA 4.9 0.9 - - - +
113A PHE* 1.3 69.5 + - - +
115A GLN* 1.3 97.0 + - + +
116A SER* 3.1 4.7 + - - -
124A SER* 3.6 16.4 - - - -
125A VAL* 3.0 45.5 + - + +
126A GLN* 6.0 1.1 - - + -
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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