Contacts of the helix formed by residues 99 - 112 (chain A) in PDB entry 3SVM
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 CYS 99 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A VAL* 4.5 7.2 - - + -
95A HIS 4.8 0.2 - - - -
96A LEU* 2.7 24.0 + - + +
97A GLU 3.2 0.2 - - - -
98A ASP* 1.3 77.5 - - - +
100A LYS* 1.3 58.2 + - - +
101A GLU 3.3 2.9 - - - -
102A VAL* 3.2 19.5 + - + -
103A LEU* 3.0 27.0 + - - +
41P PRO* 4.8 2.5 - - - -
42P SER* 3.2 11.0 - - - -
43P THR* 4.0 9.2 - - - +
44P THR 3.1 37.9 - - - -
45P ALA* 4.3 10.3 - - - -
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Residues in contact with LYS 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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97A GLU 3.8 20.0 - - - +
98A ASP* 3.4 5.2 + - - -
99A CYS* 1.3 72.7 - - - +
101A GLU* 1.3 64.2 + - - +
103A LEU* 3.7 12.5 - - + +
104A LEU* 2.9 27.0 + - - +
41P PRO* 4.3 11.8 - - + +
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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 CYS 3.3 1.0 - - - -
100A LYS* 1.3 76.9 - - - +
102A VAL* 1.3 61.7 + - + +
104A LEU* 3.8 6.9 - - - +
105A GLU* 3.2 27.7 + - - +
40P GLU* 4.4 5.4 - - - +
41P PRO* 3.1 48.7 - - + +
43P THR* 4.8 12.0 + - - -
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Residues in contact with VAL 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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61A VAL* 4.2 24.7 - - + +
62A GLU 4.6 10.3 - - - +
63A LYS* 3.9 9.2 - - + -
64A ILE* 3.7 38.9 + - + +
96A LEU* 5.1 0.7 - - + -
99A CYS* 3.2 23.3 + - + +
100A LYS 3.2 0.2 - - - -
101A GLU* 1.3 80.5 - - + +
103A LEU* 1.3 64.4 + - - +
105A GLU* 3.4 6.9 + - - +
106A PHE* 3.2 21.7 + - - +
43P THR* 5.6 6.7 - - - +
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Residues in contact with LEU 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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64A ILE* 3.7 25.6 - - + -
76A TYR* 3.8 27.8 - - + +
96A LEU* 3.2 28.5 - - + +
97A GLU* 3.9 20.0 - - - +
99A CYS* 3.0 18.8 + - + +
100A LYS* 3.4 11.9 + - + +
102A VAL* 1.3 74.8 - - - +
104A LEU* 1.3 62.8 + - - +
106A PHE* 3.4 5.6 + - + +
107A ARG* 3.1 22.2 + - - +
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Residues in contact with LEU 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 LYS 2.9 18.9 + - - +
101A GLU* 3.8 7.0 - - - +
103A LEU* 1.3 76.7 - - - +
105A GLU* 1.3 64.2 + - - +
107A ARG* 3.1 31.1 + - - +
108A LYS* 3.1 56.4 + - - +
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Residues in contact with GLU 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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63A LYS* 6.1 6.7 - - + -
101A GLU 3.2 15.4 + - - +
102A VAL* 3.4 6.9 + - - +
104A LEU* 1.3 79.6 - - - +
106A PHE* 1.3 58.3 + - - +
108A LYS* 3.8 26.6 + - - +
109A LYS* 3.2 25.3 + - + +
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Residues in contact with PHE 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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64A ILE* 3.5 38.1 - - + +
65A LEU 3.8 7.9 - - - -
66A ASP* 3.6 40.2 - - - -
67A MET* 3.8 29.6 - - + -
76A TYR* 4.2 14.1 - + - -
102A VAL 3.2 15.2 + - - +
103A LEU* 3.7 5.6 - - + +
104A LEU 3.1 0.6 - - - -
105A GLU* 1.3 76.9 - - - +
107A ARG* 1.3 66.4 + - - +
108A LYS 3.2 0.4 - - - -
109A LYS* 3.5 16.2 + - + +
110A ILE* 3.2 39.7 + - + +
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Residues in contact with ARG 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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103A LEU 3.1 14.7 + - - +
104A LEU* 3.1 28.5 + - - +
106A PHE* 1.3 79.8 - - - +
108A LYS* 1.3 76.3 + - - +
110A ILE* 2.9 27.4 - - + +
111A ALA* 3.0 25.4 + - + +
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Residues in contact with LYS 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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104A LEU* 3.1 45.7 + - - +
105A GLU* 3.9 27.1 + - - +
106A PHE 3.2 0.2 - - - -
107A ARG* 1.3 89.6 - - - +
109A LYS* 1.3 67.5 + - - +
110A ILE 3.0 2.0 - - - -
111A ALA* 2.8 18.3 + - - +
112A GLU* 2.9 21.1 + - - +
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Residues in contact with LYS 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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63A LYS* 5.9 4.2 - - - +
64A ILE 4.7 3.4 + - - +
65A LEU* 3.3 32.3 + - - +
66A ASP* 4.7 3.9 + - - -
105A GLU* 3.2 21.4 + - - +
106A PHE* 3.5 19.7 + - + +
108A LYS* 1.3 78.8 - - - +
110A ILE* 1.3 59.2 + - - +
112A GLU* 3.5 14.1 - - - +
113A ASN* 2.6 43.7 - - - +
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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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67A MET* 5.2 10.5 - - + -
106A PHE* 3.2 36.4 + - + +
107A ARG* 2.9 31.4 - - + +
108A LYS 3.0 0.6 - - - -
109A LYS* 1.3 77.4 - - + +
111A ALA* 1.3 65.5 + - + +
113A ASN* 3.4 5.8 + - + +
114A LYS* 3.1 22.6 + - + +
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Residues in contact with ALA 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 ARG* 3.0 30.4 + - - +
108A LYS* 2.8 7.9 + - - +
110A ILE* 1.3 75.6 - - + +
112A GLU* 1.3 58.0 + - - +
113A ASN 3.1 8.6 + - - -
114A LYS* 3.4 20.0 + - - +
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Residues in contact with GLU 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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108A LYS* 2.9 23.3 + - - +
109A LYS* 3.5 12.3 - - - +
111A ALA* 1.3 75.9 - - - +
113A ASN* 1.3 73.5 + - - +
114A LYS 5.5 0.4 - - - -
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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