Contacts of the helix formed by residues 101 - 115 (chain L) in PDB entry 5MS0
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 LYS 101 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100L TYR* 1.3 76.5 - - - +
102L VAL* 1.3 65.1 + - - +
103L ALA 3.6 0.4 - - - -
104L ILE* 4.0 7.7 + - - +
105L ASN* 3.5 12.0 + - - +
8R U 2.8 49.6 + - + +
9R C 6.0 6.7 - - + -
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Residues in contact with VAL 102 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99L PRO* 5.0 13.7 - - + +
100L TYR 3.5 1.8 - - - +
101L LYS* 1.3 77.1 - - - +
103L ALA* 1.3 58.4 + - - +
105L ASN* 2.9 18.7 + - - +
106L GLU* 3.0 15.4 + - - +
8R U 3.5 38.1 + - + +
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Residues in contact with ALA 103 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88L ALA* 5.8 3.1 - - - +
91L GLU* 5.1 15.7 - - + -
99L PRO 4.9 8.9 + - - +
100L TYR 4.6 3.7 + - - +
101L LYS 3.6 0.2 - - - -
102L VAL* 1.3 75.1 - - + +
104L ILE* 1.3 60.6 + - - +
106L GLU* 4.8 2.7 - - - +
107L ALA* 3.2 26.2 - - - +
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Residues in contact with ILE 104 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88L ALA* 6.4 1.6 - - - -
100L TYR 4.3 12.9 + - - +
101L LYS* 4.0 9.1 + - - +
102L VAL 3.2 0.6 - - - -
103L ALA* 1.3 79.5 - - - +
105L ASN* 1.3 59.5 + - + +
107L ALA* 3.4 1.8 + - - +
108L ILE* 2.9 31.2 + - - +
127L LEU* 5.7 9.2 - - + -
9R C 5.8 8.3 - - + -
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Residues in contact with ASN 105 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101L LYS 3.5 16.1 + - - +
102L VAL 2.9 4.0 + - - +
104L ILE* 1.3 78.3 - - + +
106L GLU* 1.3 61.4 + - - +
108L ILE* 3.4 3.1 + - - +
109L GLU* 2.9 30.0 + - - +
7R A 5.5 2.9 - - - +
8R U 3.8 27.1 - - - +
9R C 5.2 12.1 - - - +
10R U 3.9 9.8 - - + +
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Residues in contact with GLU 106 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7L ARG* 5.5 12.1 - - + -
102L VAL 3.0 13.3 + - - +
103L ALA* 5.5 1.8 - - - -
105L ASN* 1.3 77.6 - - - +
107L ALA* 1.3 57.4 + - - +
108L ILE 3.4 0.2 - - - -
109L GLU* 4.4 5.3 - - - +
110L LEU* 2.7 28.2 + - - +
7R A 5.1 22.8 + - + +
8R U 5.1 1.5 + - - +
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Residues in contact with ALA 107 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10L ARG* 6.0 5.4 - - + -
84L VAL* 4.9 10.4 - - + +
88L ALA* 6.1 4.3 - - + -
103L ALA* 3.2 23.3 + - - +
104L ILE* 3.4 3.0 + - - +
105L ASN 3.2 0.6 - - - -
106L GLU* 1.3 78.0 - - - +
108L ILE* 1.3 60.2 + - - +
110L LEU* 3.8 6.8 - - - +
111L ALA* 2.8 28.5 + - - +
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Residues in contact with ILE 108 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104L ILE 2.9 17.3 + - - +
105L ASN* 4.2 3.8 - - - +
107L ALA* 1.3 78.8 - - - +
109L GLU* 1.3 58.5 + - - +
111L ALA* 3.6 5.7 - - - +
112L LYS* 2.9 28.6 + - - +
119L SER 6.0 0.4 - - - -
120L HIS* 4.4 13.2 - - + +
123L VAL* 5.0 15.3 - - + -
124L ASN* 5.9 2.5 - - + +
9R C 6.1 0.4 - - - +
10R U 4.2 12.3 + - + +
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Residues in contact with GLU 109 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105L ASN 2.9 18.1 + - - +
106L GLU* 4.4 4.9 - - - +
108L ILE* 1.3 75.9 - - - +
110L LEU* 1.3 61.7 + - - +
112L LYS* 4.1 5.3 - - - +
113L SER* 3.4 21.5 + - - -
7R A 5.5 12.6 - - + +
10R U 3.5 18.5 + - - +
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Residues in contact with LEU 110 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11L GLU* 6.4 3.4 - - + -
106L GLU 2.7 24.1 + - - +
107L ALA* 3.8 8.5 - - - +
109L GLU* 1.3 77.7 - - - +
111L ALA* 1.3 57.5 + - - +
113L SER* 3.4 4.1 + - - -
114L PHE* 2.9 34.5 + - + +
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Residues in contact with ALA 111 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81L GLU* 6.5 0.4 - - - -
84L VAL* 4.4 19.3 - - + -
107L ALA 2.8 23.8 + - - +
108L ILE* 3.5 6.7 + - - -
109L GLU 3.4 0.2 - - - -
110L LEU* 1.3 73.6 - - - +
112L LYS* 1.3 61.0 + - - +
114L PHE* 4.9 1.1 - - - -
115L GLY* 2.9 29.1 + - - +
119L SER* 3.8 19.4 - - - +
123L VAL* 5.6 5.6 - - + -
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Residues in contact with LYS 112 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44E THR* 5.7 0.9 - - - -
108L ILE 2.9 19.0 + - - +
109L GLU* 4.1 7.0 - - - +
111L ALA* 1.3 79.2 - - - +
113L SER* 1.3 60.7 + - - +
115L GLY 4.2 2.8 + - - +
116L ALA 4.4 9.5 - - - +
117L GLU 5.6 0.5 - - - +
118L ASP 4.5 12.2 - - - +
119L SER* 4.7 1.0 + - - -
120L HIS* 3.8 21.3 - - + -
10R U 5.5 5.2 - - - +
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Residues in contact with SER 113 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43E PRO* 4.6 4.4 - - - +
44E THR* 3.4 30.9 + - - +
109L GLU 3.4 13.6 + - - -
110L LEU* 3.4 6.0 + - - -
112L LYS* 1.3 78.5 - - - +
114L PHE* 1.3 58.2 + - - +
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Residues in contact with PHE 114 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41E PRO* 5.8 3.5 - - - +
42E LEU 4.8 8.2 - - - +
43E PRO* 5.0 8.1 - - + -
44E THR* 4.7 8.0 - - - +
80L VAL* 4.8 4.9 - - - +
110L LEU* 2.9 18.0 + - + +
111L ALA* 4.9 1.1 - - - -
113L SER* 1.3 79.7 - - - +
115L GLY* 1.3 66.1 + - - +
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Residues in contact with GLY 115 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44E THR* 4.7 9.2 - - - -
80L VAL* 4.1 20.9 - - - -
81L GLU 5.7 0.4 - - - -
111L ALA* 2.9 20.9 + - - +
112L LYS 4.2 0.9 + - - +
113L SER 3.8 0.8 - - - -
114L PHE* 1.3 83.0 - - - +
116L ALA* 1.3 67.8 + - - +
119L SER* 4.7 1.3 - - - -
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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