Contacts of the helix formed by residues 125 - 140 (chain E) in PDB entry 1M63
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 PHE 125 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50E LEU 6.0 0.4 - - - -
53E GLU* 3.6 19.5 - - + -
93E GLY 3.2 20.9 + - - +
94E GLN* 5.6 2.0 - - - -
95E PHE* 3.9 11.7 - - + -
96E PHE* 4.0 20.2 - + - -
123E GLY 3.0 2.0 + - - -
124E TYR* 1.3 84.3 - - + +
126E SER* 1.3 64.9 + - - +
127E ILE 3.4 0.7 - - - -
128E GLU* 3.2 29.0 + - + +
129E CYS* 3.5 4.2 + - - -
165E GLU* 3.2 7.4 - - - -
169E LYS* 3.5 12.8 - - - -
339E HIS* 4.3 11.4 - + + -
340E PRO* 3.4 54.3 - - + -
342E TRP* 3.3 26.9 - + - -
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Residues in contact with SER 126 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93E GLY* 3.7 9.9 - - - -
119E TYR 4.3 0.9 - - - -
120E VAL* 3.6 7.3 - - - +
121E ASP* 2.9 30.5 + - - -
123E GLY 3.1 15.1 + - - -
125E PHE* 1.3 76.3 - - - +
127E ILE* 1.3 61.1 + - - -
129E CYS* 3.3 12.1 + - - +
130E VAL* 3.2 19.8 + - - +
161E THR 5.7 0.2 - - - -
162E PHE* 3.6 20.7 - - - +
165E GLU* 2.8 17.5 + - - -
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Residues in contact with ILE 127 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65E ILE* 5.0 1.6 - - + -
126E SER* 1.3 74.2 - - - +
128E GLU* 1.3 76.2 + - - +
130E VAL* 3.2 6.5 + - + +
131E LEU* 3.0 38.0 + - + +
162E PHE* 3.7 17.6 - - + -
165E GLU* 3.0 19.5 + - + +
166E CYS* 3.7 12.1 - - - -
169E LYS* 3.7 18.8 - - + -
170E TYR* 4.0 30.3 - - + -
174E VAL* 4.5 8.5 - - + -
178E CYS* 3.7 30.1 - - - -
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Residues in contact with GLU 128 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50E LEU* 4.0 39.5 - - + +
53E GLU* 4.8 8.7 - - - +
54E GLY 4.3 12.1 - - - +
55E ARG* 5.4 2.9 - - - +
95E PHE* 3.5 32.8 - - + -
125E PHE* 3.2 21.3 + - + +
127E ILE* 1.3 84.2 - - - +
129E CYS* 1.3 58.7 + - - +
131E LEU* 3.5 8.3 + - - +
132E TYR* 3.0 24.8 + - - +
169E LYS* 2.8 35.9 + - - +
170E TYR* 5.3 3.5 + - - -
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Residues in contact with CYS 129 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91E ILE* 3.5 30.1 - - + -
93E GLY* 3.3 32.5 - - - -
95E PHE* 3.7 22.2 - - - -
98E LEU* 4.3 7.0 - - + -
119E TYR* 3.6 16.8 - - + +
125E PHE 3.5 1.5 + - - -
126E SER 3.3 9.7 + - - +
128E GLU* 1.3 78.9 - - - +
130E VAL* 1.3 59.1 + - - +
132E TYR 4.2 0.7 - - - -
133E LEU* 3.3 32.9 + - - +
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Residues in contact with VAL 130 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65E ILE* 5.1 7.2 - - + -
119E TYR* 5.2 3.4 - - + -
120E VAL* 3.8 22.9 - - + -
126E SER 3.2 17.3 - - - +
127E ILE* 3.5 13.9 - - + +
128E GLU 3.2 0.4 - - - -
129E CYS* 1.3 76.8 - - + +
131E LEU* 1.3 59.6 + - + +
132E TYR 3.2 0.3 + - - -
133E LEU 3.3 0.9 + - - -
134E TRP* 2.9 67.8 + - + +
162E PHE* 4.3 5.8 - - + -
178E CYS* 4.2 15.3 - - - -
182E PHE* 4.1 17.3 - - + -
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Residues in contact with LEU 131 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46E LEU* 4.1 3.9 - - + +
50E LEU* 4.5 19.1 - - + -
56E LEU* 3.8 33.0 - - + -
61E ALA* 3.8 27.4 - - + +
64E ILE* 3.6 21.2 - - + +
65E ILE* 4.5 9.6 - - + -
127E ILE* 3.0 29.0 + - + +
128E GLU* 4.0 6.1 - - + +
130E VAL* 1.3 79.0 - - + +
132E TYR* 1.3 55.9 + - - +
134E TRP* 4.7 0.2 - - - -
135E ALA* 3.1 26.2 + - - +
170E TYR* 3.9 27.6 - - + +
174E VAL* 6.2 0.4 - - + -
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Residues in contact with TYR 132 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43E VAL* 3.7 37.7 + - + +
44E ASP* 5.0 2.9 + - - -
46E LEU* 4.8 8.5 - - + -
47E LYS* 4.0 30.2 + - + +
50E LEU* 4.3 9.2 - - + -
95E PHE* 3.8 11.2 - + + -
98E LEU* 4.3 5.8 - - + -
99E MET* 3.7 24.2 - - + -
102E PHE* 3.6 24.4 - + - +
108E PRO* 5.2 5.8 - - + +
128E GLU 3.0 17.4 + - - +
131E LEU* 1.3 75.7 - - - +
133E LEU* 1.3 62.0 + - - +
135E ALA* 3.3 3.1 + - - +
136E LEU* 3.0 63.0 + - + +
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Residues in contact with LEU 133 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91E ILE* 5.4 1.6 - - + -
98E LEU* 4.5 12.8 - - + -
102E PHE* 4.0 16.6 - - + -
115E PHE* 3.7 39.5 - - + -
119E TYR* 3.7 33.4 - - + -
129E CYS* 3.3 22.5 + - + +
130E VAL 3.3 2.1 + - - +
132E TYR* 1.3 77.4 - - - +
134E TRP* 1.3 64.4 + - + +
136E LEU* 3.3 10.8 + - + +
137E LYS* 2.9 26.7 + - - +
144E LEU* 3.9 5.0 - - + +
146E LEU* 3.8 23.6 - - + +
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Residues in contact with TRP 134 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64E ILE* 4.1 17.0 - - + +
65E ILE* 3.5 31.2 + - + -
68E GLY* 3.9 14.4 - - - -
72E LEU* 3.8 25.9 - - + +
119E TYR* 4.3 17.9 - + - -
130E VAL* 2.9 50.2 + - + +
133E LEU* 1.3 79.2 - - + +
135E ALA* 1.3 63.5 + - - +
136E LEU 3.2 0.4 - - - -
137E LYS* 3.2 14.2 + - + +
138E ILE* 3.2 21.0 + - - +
146E LEU* 4.1 17.5 - - + -
181E ALA* 3.7 23.0 - - + +
182E PHE* 3.7 30.3 - + - -
185E LEU* 3.8 25.4 - - + -
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Residues in contact with ALA 135 (chain E).
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* 3.5 24.4 - - + +
43E VAL* 4.2 11.1 - - + +
46E LEU* 3.6 23.8 - - + -
64E ILE* 3.9 10.5 - - + +
131E LEU 3.1 23.1 + - - +
132E TYR* 3.6 5.2 - - + +
133E LEU 3.3 0.2 - - - -
134E TRP* 1.3 76.7 - - - +
136E LEU* 1.3 61.6 + - - +
138E ILE* 3.6 3.1 + - - -
139E LEU* 3.4 18.7 + - - +
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Residues in contact with LEU 136 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43E VAL* 3.9 24.0 - - + -
102E PHE* 3.7 23.6 - - + -
108E PRO* 3.9 26.9 - - + -
132E TYR* 3.0 52.4 + - + +
133E LEU* 3.5 10.3 - - + +
134E TRP 3.2 0.2 - - - -
135E ALA* 1.3 78.8 - - - +
137E LYS* 1.3 56.7 - - - +
139E LEU* 4.8 0.2 - - - -
140E TYR* 2.9 46.8 + - + +
144E LEU* 3.8 20.7 - - + +
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Residues in contact with LYS 137 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68E GLY* 4.5 9.4 - - - +
71E ILE* 4.3 17.7 - - + +
72E LEU* 3.8 22.4 - - + +
75E GLU* 2.9 42.1 + - - -
133E LEU 2.9 16.4 + - - +
134E TRP* 3.2 12.5 + - + +
136E LEU* 1.3 75.6 - - - +
138E ILE* 1.3 64.0 + - + +
140E TYR 4.1 2.7 - - - +
141E PRO* 3.4 31.9 + - - +
144E LEU* 3.1 28.0 + - - +
145E PHE* 3.9 12.3 - - - +
146E LEU* 4.1 19.8 - - + +
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Residues in contact with ILE 138 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35E PHE* 4.5 10.3 - - + -
39E GLY 4.3 9.2 - - - +
40E LYS* 4.9 9.0 - - + +
41E PRO* 4.0 18.6 - - + -
64E ILE* 3.6 31.4 - - + +
67E GLU* 3.8 26.5 - - + +
68E GLY* 3.9 16.2 - - - +
71E ILE* 3.9 19.5 - - + +
134E TRP 3.2 13.6 + - - +
135E ALA* 3.9 9.0 - - - +
136E LEU 3.3 0.2 - - - -
137E LYS* 1.3 79.8 - - - +
139E LEU* 1.3 62.2 + - - +
141E PRO* 3.3 13.0 - - - +
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Residues in contact with LEU 139 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40E LYS* 3.9 39.5 - - + +
41E PRO* 3.4 25.5 - - + +
42E ARG* 5.5 0.2 - - - -
43E VAL* 3.9 21.1 - - + -
135E ALA 3.4 13.4 + - - +
136E LEU* 4.8 0.4 - - - -
138E ILE* 1.3 80.0 - - - +
140E TYR* 1.3 95.4 + - + +
141E PRO* 3.7 4.7 - - - +
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Residues in contact with TYR 140 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43E VAL* 5.0 6.2 - - + +
108E PRO* 3.6 38.0 - - + +
109E ALA* 3.7 26.6 + - + +
136E LEU* 2.9 35.6 + - + +
137E LYS 3.5 4.4 - - - +
139E LEU* 1.3 112.9 - - + +
141E PRO* 1.4 64.0 - - - +
142E LYS 3.5 2.2 - - - -
143E THR* 3.8 24.5 - - + -
144E LEU* 3.3 26.3 + - + +
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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