Contacts of the helix formed by residues 102 - 108 (chain M) in PDB entry 5X6E
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 LEU 102 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8M PHE* 5.6 4.0 - - + -
38M CYS* 3.7 20.0 - - + -
70M MET* 3.5 32.3 - - + -
74M ILE* 4.4 13.5 - - + -
97M ILE* 3.7 22.6 - - + +
98M LYS 3.8 9.9 + - - +
99M ILE* 3.7 17.0 - - + +
101M GLU* 1.3 75.5 - - - +
103M LYS* 1.3 53.4 + - - +
104M GLU 3.2 1.1 - - - -
105M LEU* 2.9 19.2 + - + +
106M LEU* 2.4 64.1 + - + +
116M VAL* 5.5 3.8 - - + -
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Residues in contact with LYS 103 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74M ILE* 3.7 28.9 - - + +
75M ASP* 4.9 15.1 + - + +
77M GLU* 5.2 8.1 + - - +
99M ILE 4.3 2.6 + - - +
100M ASN 4.6 5.8 - - - +
101M GLU 2.3 23.3 + - - +
102M LEU* 1.3 70.1 - - - +
104M GLU* 1.3 60.7 + - + +
106M LEU* 4.0 7.6 - - - +
107M SER* 2.7 33.8 + - - -
114N PHE* 3.7 30.5 - - + -
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Residues in contact with GLU 104 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100M ASN 5.1 2.5 - - - +
101M GLU* 3.2 25.9 + - - +
103M LYS* 1.3 85.2 - - + +
105M LEU* 1.3 66.2 + - + +
106M LEU 3.3 1.2 + - - -
107M SER* 3.5 14.8 + - - -
108M LYS* 3.9 6.2 + - - +
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Residues in contact with LEU 105 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8M PHE* 6.4 0.2 - - + -
11M TYR* 3.5 28.1 + - + +
12M LEU* 4.9 8.1 - - + -
15M ASN* 3.9 25.4 - - + +
17M ILE* 3.6 29.4 - - + -
97M ILE* 4.8 11.0 - - + -
101M GLU* 4.3 19.1 - - + +
102M LEU* 2.9 26.2 + - + +
104M GLU* 1.3 85.2 - - + +
106M LEU* 1.3 59.5 + - + +
108M LYS* 3.1 27.8 + - - +
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Residues in contact with LEU 106 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8M PHE* 4.8 7.9 - - + -
74M ILE* 4.2 19.1 - - + -
102M LEU* 2.4 54.5 + - + +
103M LYS* 4.1 5.8 - - - -
105M LEU* 1.3 77.3 - - - +
107M SER* 1.3 69.9 + - - +
108M LYS* 3.4 6.4 - - - +
112M HIS 3.8 11.2 - - - +
113M PHE* 3.0 70.7 - - + +
116M VAL* 4.1 26.0 - - + -
114N PHE* 5.0 0.4 - - + -
117N PHE* 4.9 1.8 - - + -
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Residues in contact with SER 107 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103M LYS 2.7 23.8 + - - -
104M GLU* 3.5 9.4 + - - -
106M LEU* 1.3 75.9 - - - +
108M LYS* 1.3 61.6 + - - +
109M ASN 2.9 10.4 + - - -
110M LEU* 3.3 14.6 - - - +
110N LEU* 3.1 32.1 - - - +
114N PHE* 4.7 5.3 - - - -
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Residues in contact with LYS 108 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11M TYR* 3.0 41.5 - - + +
104M GLU 3.9 4.4 + - - +
105M LEU 3.1 23.7 + - - +
106M LEU* 3.4 6.1 - - - +
107M SER* 1.3 78.7 + - - +
109M ASN* 1.3 110.4 + - + +
112M HIS* 3.1 47.1 + - - +
113M PHE* 3.7 5.7 - - - +
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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