Contacts of the helix formed by residues 77 - 95 (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 ASN 77 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499 G 3.3 17.7 - - - +
509 G 3.0 36.0 + - - +
43M VAL* 5.2 0.7 - - - +
71M TRP* 4.7 2.9 - - - -
73M ALA* 5.5 1.6 - - - +
74M PRO* 3.5 25.7 + - - +
75M THR 3.5 1.4 + - - -
76M GLY* 1.3 72.8 - - - +
78M MET* 1.3 68.5 + - - +
79M PRO* 3.6 11.5 - - + +
80M SER* 2.9 39.0 + - - -
81M ALA* 3.0 22.2 + - - +
114M LYS* 3.9 5.5 - - - +
146M HIS* 5.8 0.4 - - + -
147M ILE* 5.0 2.6 - - + +
159M TYR* 3.9 5.1 + - - -
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Residues in contact with MET 78 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489 C 3.9 9.9 - - - +
499 G 3.0 20.3 + - - +
77M ASN* 1.3 76.8 - - - +
79M PRO* 1.3 69.4 - - + +
81M ALA* 3.1 4.7 + - - +
82M TYR* 3.0 22.3 + - - +
112M GLY 3.1 29.4 - - - +
113M SER 3.8 11.9 - - - +
114M LYS* 3.6 24.0 - - + -
117M ALA* 4.1 15.5 - - + +
137M ALA* 3.6 26.0 - - + +
141M ARG* 3.7 23.3 - - + +
142M THR* 3.9 8.3 - - - +
146M HIS* 4.1 8.3 - - + +
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Residues in contact with PRO 79 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71M TRP* 4.5 11.9 - - + -
77M ASN* 3.6 15.0 - - + +
78M MET* 1.3 94.1 - - + +
80M SER* 1.3 60.8 + - - +
82M TYR* 3.6 1.1 + - + -
83M LEU* 3.0 32.9 + - - +
142M THR 2.9 22.9 - - - +
143M ARG 3.3 4.3 - - - +
144M GLY* 3.3 26.5 - - - -
146M HIS* 4.5 2.7 - - + -
147M ILE* 6.0 0.9 - - + -
172M PHE* 3.6 20.6 - - + -
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Residues in contact with SER 80 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43M VAL* 5.0 0.8 - - - +
63M SER* 3.5 12.5 - - - -
66M LEU* 4.0 13.8 - - - +
71M TRP* 4.7 3.3 - - - -
74M PRO 4.4 2.0 - - - -
75M THR* 2.8 38.4 + - - -
77M ASN* 2.9 28.4 + - - -
79M PRO* 1.3 77.9 - - - +
81M ALA* 1.3 63.6 + - - +
83M LEU* 3.3 5.8 + - - +
84M THR* 2.9 26.6 + - - -
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Residues in contact with ALA 81 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43M VAL* 3.7 20.3 - - + +
77M ASN 3.0 12.4 + - - +
78M MET 3.5 7.9 - - - +
80M SER* 1.3 75.8 - - - +
82M TYR* 1.3 63.8 + - - +
84M THR* 3.2 3.8 + - - -
85M GLY* 2.9 18.0 + - - -
114M LYS* 3.6 37.9 - - + +
117M ALA* 4.1 2.2 - - + -
118M ILE* 3.7 16.5 - - + +
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Residues in contact with TYR 82 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78M MET 3.0 10.4 + - - +
79M PRO 3.9 3.8 - - - +
80M SER 3.3 0.2 - - - -
81M ALA* 1.3 74.6 - - - +
83M LEU* 1.3 66.1 + - + +
85M GLY* 2.9 4.3 + - - -
86M LEU* 2.8 48.6 + - + +
117M ALA* 3.6 17.4 - - + +
120M GLU* 4.0 10.3 - - + -
121M GLY* 3.6 24.6 - - - -
124M ASP* 2.8 29.2 + - - +
139M TRP* 4.0 11.2 - + - -
142M THR* 3.6 33.0 - - + -
172M PHE* 3.8 15.7 - + + -
176M ARG* 2.6 41.2 + - - -
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Residues in contact with LEU 83 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66M LEU* 3.9 20.0 - - + -
71M TRP* 3.7 23.8 - - + -
79M PRO 3.0 20.8 + - - +
80M SER 3.7 2.7 - - - +
82M TYR* 1.3 83.2 - - + +
84M THR* 1.3 57.6 + - - +
86M LEU* 3.6 4.8 - - + +
87M LEU* 2.8 31.5 + - - +
172M PHE* 3.7 23.6 - - + -
175M LEU* 3.4 24.2 - - + -
176M ARG* 3.9 30.5 - - + +
179M LEU* 4.1 13.1 - - + +
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Residues in contact with THR 84 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43M VAL* 3.3 26.0 - - + +
45M ALA* 4.1 6.5 - - + +
61M ALA* 3.2 37.5 - - + +
62M HIS 3.8 1.6 - - - +
63M SER* 3.3 26.6 - - - +
66M LEU* 4.1 6.6 - - - +
80M SER 2.9 17.9 + - - -
81M ALA 3.6 4.7 - - - -
83M LEU* 1.3 76.6 - - - +
85M GLY* 1.3 57.3 + - - +
87M LEU* 4.3 4.7 - - - -
88M ALA* 3.0 25.3 + - - +
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Residues in contact with GLY 85 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45M ALA* 4.5 3.6 - - - -
81M ALA 2.9 9.0 + - - -
82M TYR 2.9 8.0 + - - -
84M THR* 1.3 76.2 - - - +
86M LEU* 1.3 53.6 + - - +
88M ALA* 3.3 2.1 + - - +
89M GLY* 2.7 33.1 + - - -
118M ILE* 3.6 30.5 - - - +
122M ALA* 3.5 14.3 - - - +
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Residues in contact with LEU 86 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82M TYR* 2.8 31.6 + - + +
83M LEU* 3.6 6.7 - - + +
85M GLY* 1.3 74.8 - - - +
87M LEU* 1.3 58.4 + - - +
90M LEU* 2.8 49.4 + - + +
121M GLY* 3.4 16.6 - - - +
124M ASP* 4.1 6.5 - - + -
125M ALA* 3.4 36.7 - - + +
176M ARG* 4.4 13.0 - - + -
179M LEU* 4.0 26.2 - - + -
180M LEU* 4.2 21.1 - - + -
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Residues in contact with LEU 87 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61M ALA* 3.8 7.0 - - + -
62M HIS 4.8 1.8 - - - +
65M ASP* 3.8 24.2 - - - +
66M LEU* 4.0 21.5 - - + -
69M TYR* 4.1 16.8 - - + +
83M LEU 2.8 17.7 + - - +
84M THR* 3.7 5.2 - - - +
86M LEU* 1.3 77.5 - - - +
88M ALA* 1.3 62.2 + - - +
90M LEU* 3.3 4.1 + - - -
91M ARG* 3.1 50.0 + - - +
179M LEU* 4.3 10.3 - - + +
186M LEU* 3.2 42.7 - - + +
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Residues in contact with ALA 88 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34M LEU* 5.5 5.4 - - + -
45M ALA* 3.6 27.6 - - + +
46M GLN* 5.4 1.3 - - - -
47M LEU* 5.3 2.4 - - + +
59M ALA* 4.3 4.0 - - - +
60M SER* 4.0 9.9 - - - +
61M ALA* 3.3 23.9 - - + +
84M THR 3.0 12.5 + - - +
85M GLY 3.8 3.1 - - - +
87M LEU* 1.3 75.4 - - - +
89M GLY* 1.3 53.0 + - - +
91M ARG* 3.2 3.7 + - - +
92M ALA* 2.7 36.1 + - - +
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Residues in contact with GLY 89 (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* 6.1 0.6 - - - +
85M GLY 2.7 22.3 + - - -
86M LEU 3.6 1.8 - - - -
87M LEU 3.2 0.4 - - - -
88M ALA* 1.3 73.6 - - - +
90M LEU* 1.3 55.7 + - - +
92M ALA* 3.0 10.0 - - - +
93M GLN* 2.9 31.4 + - - +
122M ALA* 4.3 4.4 - - - +
125M ALA* 3.5 15.9 - - - -
127M LEU* 4.0 14.9 - - - +
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Residues in contact with LEU 90 (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* 2.8 35.9 + - + +
87M LEU* 4.6 0.7 - - - -
88M ALA 3.3 0.2 - - - -
89M GLY* 1.3 69.6 - - - +
91M ARG* 1.3 65.9 + - - +
93M GLN* 3.1 8.5 + - + +
94M GLU* 3.0 24.9 + - - +
125M ALA* 3.4 29.6 - - + +
179M LEU* 3.2 37.7 - - + +
180M LEU* 5.2 6.3 - - + -
186M LEU* 3.4 38.2 - - + +
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Residues in contact with ARG 91 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59M ALA* 3.9 12.6 - - + +
60M SER 3.0 27.8 + - - +
61M ALA* 3.5 11.3 - - - +
65M ASP* 3.0 28.6 + - - -
68M GLU* 4.7 1.2 + - - -
69M TYR* 3.3 24.9 + - - -
87M LEU* 3.1 31.5 + - - +
88M ALA* 3.6 6.5 - - - +
90M LEU* 1.3 75.4 - - - +
92M ALA* 1.3 64.1 + - - +
94M GLU* 3.2 10.3 + - - +
95M ALA* 3.0 22.0 + - - +
185M GLU* 3.3 43.4 + - - +
186M LEU* 3.5 4.3 - - + +
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Residues in contact with ALA 92 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47M LEU* 3.2 35.9 - - + -
59M ALA* 3.6 11.9 - - + +
88M ALA 2.7 14.8 + - - +
89M GLY 3.0 14.6 - - - +
91M ARG* 1.3 76.7 - - - +
93M GLN* 1.3 60.2 + - - +
95M ALA* 2.9 12.5 + - - +
96M GLY 3.3 0.2 + - - -
97M VAL* 3.0 21.4 + - + +
127M LEU* 3.7 9.2 - - + -
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Residues in contact with GLN 93 (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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89M GLY 2.9 17.2 + - - +
90M LEU* 3.1 10.1 + - + +
92M ALA* 1.3 74.4 - - - +
94M GLU* 1.3 60.3 + - + +
96M GLY* 2.8 22.0 + - - -
97M VAL 2.7 30.0 + - - -
98M GLU* 3.8 12.0 + - - +
125M ALA 3.8 18.4 - - - +
126M GLY* 4.0 20.7 + - - +
127M LEU* 3.3 13.8 - - + +
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Residues in contact with GLU 94 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90M LEU 3.0 10.4 + - - +
91M ARG* 3.4 11.4 - - - +
93M GLN* 1.3 77.6 - - + +
95M ALA* 1.3 58.2 + - - +
96M GLY* 3.2 4.2 + - - -
186M LEU* 2.9 38.7 - - - +
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Residues in contact with ALA 95 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58M LEU* 3.8 27.9 - - + +
91M ARG 3.0 11.6 + - - +
92M ALA* 2.9 11.5 + - - +
94M GLU* 1.3 75.1 - - - +
96M GLY* 1.3 59.9 + - - +
97M VAL* 3.8 10.4 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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