Contacts of the helix formed by residues 113 - 125 (chain M) in PDB entry 1JJ2
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 SER 113 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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369 C 4.8 0.7 - - - -
479 A 3.6 11.4 + - - -
489 C 3.6 12.1 - - - -
78M MET* 3.8 5.3 - - - +
108M SER 4.0 4.0 + - - -
110M THR* 2.6 43.3 + - - +
111M PRO 3.2 0.4 + - - -
112M GLY* 1.3 82.8 - - - +
114M LYS* 1.3 65.3 + - - +
115M VAL* 3.4 20.2 - - - -
116M PHE* 3.5 6.7 + - - +
117M ALA* 3.3 15.8 + - - +
137M ALA 5.8 0.2 + - - -
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Residues in contact with LYS 114 (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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489 C 2.7 39.2 + - - +
499 G 3.5 18.6 + - - +
38M LYS* 3.6 28.5 - - + +
39M SER 4.9 8.9 + - - -
40M ASN 5.8 0.8 + - - -
43M VAL* 4.5 10.7 - - + +
76M GLY* 3.5 21.4 + - - -
77M ASN* 3.9 15.3 - - - +
78M MET* 3.6 22.9 - - - -
81M ALA* 3.6 10.7 - - + +
113M SER* 1.3 70.3 - - - +
115M VAL* 1.3 60.4 + - - +
116M PHE 3.2 0.4 - - - -
117M ALA* 3.0 5.3 + - - +
118M ILE* 2.8 33.3 + - - +
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Residues in contact with VAL 115 (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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489 C 4.7 0.2 + - - -
36M ALA* 4.0 18.8 - - + +
38M LYS* 4.6 15.0 - - + -
102M LEU* 4.2 6.9 - - - +
104M ILE* 3.9 26.5 - - + -
107M ASN* 4.1 30.1 - - + +
108M SER 4.5 11.4 - - - +
113M SER* 4.1 16.2 - - - -
114M LYS* 1.3 77.9 - - - +
116M PHE* 1.3 70.5 + - + +
118M ILE* 3.3 12.7 - - + +
119M GLN* 3.0 24.3 + - - +
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Residues in contact with PHE 116 (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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24130 A 3.6 50.9 - + - -
102M LEU* 3.8 12.1 - - + -
104M ILE* 5.0 1.1 - - + -
109M PRO* 3.5 26.5 - - + -
110M THR 3.3 26.9 - - - -
113M SER* 3.5 12.0 + - - +
114M LYS 3.2 0.6 - - - -
115M VAL* 1.3 82.7 - - + +
117M ALA* 1.3 60.7 + - - +
119M GLN* 3.2 20.7 + - - +
120M GLU* 2.8 27.4 + - - +
135M VAL* 3.4 31.6 - - + +
136M LEU* 3.9 21.4 - - + +
137M ALA 6.2 0.2 - - - -
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Residues in contact with ALA 117 (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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78M MET* 4.1 21.8 - - + +
81M ALA* 4.1 11.0 - - + -
82M TYR* 3.6 20.2 - - + +
113M SER 3.3 13.1 + - - +
114M LYS* 3.0 14.0 + - - +
116M PHE* 1.3 74.1 - - - +
118M ILE* 1.3 66.9 + - - +
120M GLU* 3.0 13.1 + - - +
121M GLY 2.9 19.4 + - - -
136M LEU* 6.3 0.2 - - - -
137M ALA 6.3 1.1 - - - +
142M THR* 4.9 4.7 - - + +
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Residues in contact with ILE 118 (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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34M LEU* 4.7 10.5 - - + -
36M ALA* 3.7 29.4 - - + -
37M ARG 4.4 5.2 - - - +
38M LYS* 5.3 0.7 - - + -
43M VAL* 3.6 25.6 - - + -
44M ARG 4.0 10.3 - - - +
45M ALA* 3.9 23.1 - - + -
81M ALA* 3.7 25.4 - - + +
85M GLY* 3.6 9.6 - - - +
102M LEU* 5.5 0.2 - - + -
114M LYS 2.8 19.4 + - - +
115M VAL* 3.3 11.9 - - + +
116M PHE 3.2 0.2 - - - -
117M ALA* 1.3 76.9 - - - +
119M GLN* 1.3 63.5 + - - +
121M GLY 3.2 1.0 + - - -
122M ALA* 3.0 21.3 + - - +
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Residues in contact with GLN 119 (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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24130 A 4.9 5.6 + - - -
24140 A 5.6 0.6 + - - -
34M LEU* 4.1 11.9 - - + -
102M LEU* 3.5 35.3 - - + +
115M VAL 3.0 12.8 + - - +
116M PHE* 3.4 26.8 - - - +
117M ALA 3.1 0.2 - - - -
118M ILE* 1.3 77.4 - - - +
120M GLU* 1.3 62.2 + - - +
122M ALA* 3.4 1.7 + - - +
123M ILE* 3.0 41.0 + - + +
129M ILE* 3.7 9.5 - - + +
130M PRO 3.2 25.1 + - - -
131M HIS* 3.6 19.4 - - - +
132M ASN 5.0 0.2 + - - -
135M VAL* 5.1 0.3 - - - +
136M LEU* 3.9 10.5 - - + +
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Residues in contact with GLU 120 (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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82M TYR* 4.0 12.8 - - + -
116M PHE 2.8 16.3 + - - +
117M ALA* 3.0 12.5 + - - +
119M GLN* 1.3 73.8 - - - +
121M GLY* 1.3 62.6 + - - +
123M ILE* 3.2 11.8 + - + +
124M ASP* 3.1 38.2 + - - +
136M LEU* 3.8 36.0 - - + +
137M ALA 4.2 7.3 + - - +
139M TRP* 4.1 18.2 + - - +
142M THR* 3.9 17.8 + - - +
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Residues in contact with GLY 121 (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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82M TYR* 3.6 40.1 - - - -
86M LEU* 3.4 15.5 - - - +
117M ALA 2.9 10.7 + - - -
118M ILE 3.7 0.9 - - - -
120M GLU* 1.3 77.3 - - - +
122M ALA* 1.3 62.6 + - - +
124M ASP* 3.1 5.4 + - - +
125M ALA 3.0 18.2 + - - -
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Residues in contact with ALA 122 (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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34M LEU* 3.6 38.6 - - + -
85M GLY 3.5 18.8 - - - +
89M GLY* 4.3 1.6 - - - -
118M ILE 3.0 10.3 + - - +
119M GLN 3.8 1.6 - - - +
121M GLY* 1.3 74.2 - - - +
123M ILE* 1.3 62.2 + - - +
125M ALA* 3.3 12.4 + - - +
127M LEU* 3.1 32.6 + - + +
129M ILE* 4.0 6.7 - - + -
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Residues in contact with ILE 123 (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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119M GLN* 3.0 31.8 + - + +
120M GLU* 3.6 10.5 - - + +
122M ALA* 1.3 75.3 - - - +
124M ASP* 1.3 63.5 + - - +
126M GLY* 3.0 20.4 + - - -
127M LEU 3.2 18.8 - - - +
128M ASP* 5.7 0.4 - - - -
129M ILE* 4.0 17.9 - - + +
131M HIS* 3.5 45.5 - - + +
136M LEU* 5.8 3.4 - - + -
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Residues in contact with ASP 124 (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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82M TYR* 2.8 33.1 + - - +
86M LEU* 4.1 5.9 - - + +
120M GLU* 3.1 26.4 + - - +
121M GLY 3.1 5.6 + - - +
123M ILE* 1.3 76.0 - - - +
125M ALA* 1.3 62.0 + - - +
126M GLY* 2.9 7.6 + - - -
139M TRP* 5.4 0.2 - - - -
176M ARG* 3.9 14.2 + - - +
180M LEU* 5.1 7.6 - - + +
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Residues in contact with ALA 125 (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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86M LEU* 3.4 39.2 - - + +
89M GLY* 3.5 6.7 - - - -
90M LEU* 3.4 31.9 - - + +
93M GLN* 3.8 12.2 - - - +
121M GLY 3.0 8.2 + - - +
122M ALA 3.4 11.7 - - - +
123M ILE 3.1 0.4 - - - -
124M ASP* 1.3 76.3 - - - +
126M GLY* 1.3 57.4 + - - +
127M LEU 3.7 0.2 - - - -
180M LEU* 5.7 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