Contacts of the helix formed by residues 102 - 113 (chain M) in PDB entry 5A15
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 GLU 102 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81M LEU* 3.9 9.6 - - + +
100M PHE* 3.1 27.9 - - + -
101M PRO* 1.3 95.8 - - + +
103M LYS* 1.3 63.4 + - - +
104M GLY 3.3 2.9 - - - +
105M ARG* 3.4 30.0 + - + -
106M LEU* 3.2 15.1 + - - +
83N ARG* 3.0 40.4 + - - -
84N TYR* 4.2 0.7 + - - -
96N LEU 5.5 0.2 - - - -
97N PRO* 3.5 23.5 - - + +
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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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96M LEU* 3.7 30.3 - - + -
100M PHE* 3.7 24.7 + - + +
101M PRO 3.7 2.2 + - - -
102M GLU* 1.3 76.6 - - - +
104M GLY* 1.3 62.9 + - - +
106M LEU* 3.4 5.8 + - - +
107M LYS* 3.1 21.3 + - - +
122M LEU* 4.5 27.9 - - + +
124M PRO* 6.4 0.4 - - - +
98N ASP* 4.3 6.7 + - - +
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Residues in contact with GLY 104 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102M GLU 3.3 0.8 - - - -
103M LYS* 1.3 80.0 - - - +
105M ARG* 1.3 60.1 + - - +
107M LYS* 3.3 22.3 - - - +
108M ARG* 3.2 16.8 + - - +
95N VAL* 3.7 19.3 - - - +
96N LEU 5.8 0.4 - - - -
98N ASP* 5.4 4.0 + - - -
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Residues in contact with ARG 105 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78M ASP* 3.8 3.0 + - - +
81M LEU* 3.7 20.5 - - + +
102M GLU* 3.4 27.2 + - + +
103M LYS 3.3 0.6 - - - -
104M GLY* 1.3 72.7 - - - +
106M LEU* 1.3 62.4 + - - +
108M ARG* 3.0 20.2 + - - +
109M GLU* 3.0 18.6 + - - +
83N ARG* 3.0 45.3 - - - +
84N TYR* 3.6 20.9 - - - -
87N ASP* 2.3 38.4 + - - +
94N VAL* 6.1 0.8 - - - +
95N VAL* 2.7 43.3 + - + +
96N LEU 3.9 5.6 - - - +
97N PRO* 4.1 10.8 - - - -
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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
----------------------------------------------------------
81M LEU* 3.7 38.9 - - + +
84M TYR* 3.9 24.0 - - + -
85M ILE* 3.7 20.9 - - + +
94M VAL* 5.3 2.0 - - + -
96M LEU* 4.5 12.8 - - + -
100M PHE* 4.4 13.0 - - + -
102M GLU 3.2 15.7 + - - +
103M LYS 3.6 5.2 - - - +
105M ARG* 1.3 78.8 - - - +
107M LYS* 1.3 57.9 + - - +
109M GLU* 3.2 2.0 + - + +
110M ALA* 2.8 27.7 + - - +
118M LEU* 5.4 3.8 - - + -
122M LEU* 3.7 27.4 - - + -
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Residues in contact with LYS 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 3.1 14.0 + - - +
104M GLY* 3.3 20.1 - - - +
105M ARG 3.1 0.2 - - - -
106M LEU* 1.3 77.2 - - - +
108M ARG* 1.3 56.7 + - - +
110M ALA* 3.2 4.6 + - - +
111M GLU* 2.9 45.0 + - - +
119M VAL* 4.3 11.0 - - + -
122M LEU* 3.8 21.9 + - + +
123M THR* 3.4 40.6 - - + +
124M PRO* 5.3 4.6 - - - +
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Residues in contact with ARG 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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24A PRO* 5.3 2.8 - - - +
25A GLU* 2.7 42.0 + - - +
77M ARG* 3.8 10.1 - - - +
104M GLY 3.2 8.3 + - - +
105M ARG* 3.0 12.2 + - - +
107M LYS* 1.3 77.9 - - - +
109M GLU* 1.3 66.7 + - - +
111M GLU* 3.2 35.9 + - - +
112M TYR* 3.0 19.4 + - - +
91N ASP* 3.0 45.6 + - - +
93N GLN* 4.3 25.0 - - + +
95N VAL* 4.2 20.4 - - + +
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Residues in contact with GLU 109 (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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77M ARG* 2.8 51.7 + - - +
78M ASP* 4.1 20.1 - - - +
81M LEU* 3.7 25.0 - - + +
85M ILE* 4.1 17.5 - - + -
105M ARG* 3.0 20.3 + - - +
106M LEU* 3.6 7.4 - - - +
108M ARG* 1.3 75.9 - - - +
110M ALA* 1.3 61.5 + - - +
112M TYR* 3.0 2.3 + - - +
113M PHE* 2.9 42.2 + - + -
87N ASP* 4.4 9.0 - - - +
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Residues in contact with ALA 110 (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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26A VAL* 4.1 0.2 - - - +
85M ILE* 3.9 8.4 - - - +
106M LEU 2.8 13.6 + - - +
107M LYS* 3.4 13.5 - - - +
109M GLU* 1.3 78.5 - - - +
111M GLU* 1.3 56.4 + - - +
113M PHE 3.5 0.9 + - - -
114M GLN 3.0 7.8 + - - -
115M LEU* 3.0 30.2 + - - +
118M LEU* 3.5 35.7 - - + -
119M VAL* 3.9 14.8 - - + +
122M LEU* 4.4 0.4 - - + -
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Residues in contact with GLU 111 (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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24A PRO* 4.6 10.7 - - - +
25A GLU* 3.0 20.6 - - - +
26A VAL* 3.6 31.4 - - + +
107M LYS* 2.9 37.2 + - - +
108M ARG* 3.2 39.5 + - - +
109M GLU 3.1 0.2 - - - -
110M ALA* 1.3 78.1 - - - +
112M TYR* 1.3 60.8 + - - +
114M GLN* 3.1 12.1 + - - -
119M VAL* 3.9 18.3 - - + +
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Residues in contact with TYR 112 (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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25A GLU* 3.1 35.0 + - - +
50M LEU* 3.2 39.8 - - + +
54M MET* 6.0 0.9 - - - -
75M ILE* 4.7 6.0 - - + +
76M ASP* 4.9 6.1 + - - +
77M ARG* 3.3 70.6 - - + +
108M ARG* 3.0 8.9 + - - +
109M GLU 3.0 7.4 + - - +
111M GLU* 1.3 78.7 - - - +
113M PHE* 1.3 72.1 + + - +
114M GLN* 3.2 12.3 + - - +
91N ASP* 4.8 0.9 - - - -
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Residues in contact with PHE 113 (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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49M SER* 3.8 4.9 - - - -
50M LEU* 3.2 26.0 + - + -
51M LEU* 4.0 29.0 + - + -
54M MET* 6.5 0.2 - - - -
75M ILE* 4.0 17.5 - - + -
77M ARG* 4.0 17.9 - - + -
82M PHE* 3.6 37.2 - + - -
85M ILE* 4.0 21.3 - - + -
109M GLU* 2.9 44.9 + - + +
110M ALA 4.2 0.2 - - - +
112M TYR* 1.3 85.1 - + - +
114M GLN* 1.3 71.7 + - - +
115M LEU* 3.6 20.9 - - + +
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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