Contacts of the helix formed by residues 76 - 95 (chain M) in PDB entry 6CM9
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 CYS 76 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220B ILE* 4.8 5.8 - - - -
224B ASP* 4.2 20.9 - - - +
258B SER* 5.0 4.3 - - - -
261B LYS* 5.7 2.0 - - - -
567B ILE 5.8 0.4 - - - -
568B GLY 3.5 15.3 - - - -
569B THR* 4.0 12.8 - - + -
2M SER* 4.0 16.3 - - - +
74M ASN 3.7 1.6 + - - -
75M ALA* 1.3 70.3 - - - +
77M VAL* 1.3 59.6 + - - +
78M SER* 4.0 9.0 - - - -
79M LEU* 3.2 27.1 + - + +
80M VAL* 3.0 30.4 + - - +
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Residues in contact with VAL 77 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B VAL* 3.7 21.1 - - + -
568B GLY 3.0 6.8 + - - +
569B THR 3.5 5.6 - - - +
570B LEU* 3.4 35.0 - - + +
573B VAL* 4.7 1.1 - - + -
49M ILE* 3.8 13.2 - - + -
58M MET* 4.2 8.7 - - + -
75M ALA 3.3 15.7 - - - +
76M CYS* 1.3 70.5 - - - +
78M SER* 1.3 61.2 + - - +
80M VAL* 3.3 5.9 + - - +
81M PHE* 2.9 62.7 + - + -
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Residues in contact with SER 78 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B SER 4.5 2.0 - - - -
254B ALA* 3.3 27.0 + - - +
257B LEU* 3.7 28.9 - - - +
258B SER* 4.5 3.8 + - - -
298B LEU* 4.3 13.8 - - - +
301B VAL* 4.5 3.9 - - - +
568B GLY* 3.5 13.2 + - - -
76M CYS* 4.0 6.8 - - - -
77M VAL* 1.3 79.0 - - - +
79M LEU* 1.3 58.7 + - - +
81M PHE* 4.2 0.3 - - - +
82M SER* 3.0 35.2 + - - -
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Residues in contact with LEU 79 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B TRP* 3.6 29.4 - - + -
220B ILE* 3.7 18.4 - - + -
221B PHE* 3.7 31.6 - - + -
224B ASP* 5.8 0.9 - - - +
254B ALA* 4.0 5.8 - - - -
2M SER* 3.6 23.6 - - - +
76M CYS* 3.2 25.2 + - + +
78M SER* 1.3 83.1 + - - +
80M VAL* 1.3 57.7 + - - +
82M SER* 3.8 0.9 - - - -
83M PHE* 2.9 30.3 + - - +
118M MET* 6.2 0.4 - - + -
121M GLY 4.5 1.6 - - - +
122M TYR* 5.0 0.7 - - + -
123M PRO* 4.0 19.3 - - + -
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Residues in contact with VAL 80 (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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2M SER 3.9 20.2 - - - +
3M ALA* 4.0 17.9 - - + +
58M MET* 3.8 46.9 - - + -
69M ALA* 4.4 13.5 - - + -
75M ALA* 4.8 0.4 - - + -
76M CYS 3.0 16.5 + - - +
77M VAL* 3.3 5.6 + - - +
79M LEU* 1.3 75.8 - - + +
81M PHE* 1.3 57.5 + - - +
83M PHE* 3.3 8.7 + - + +
84M LEU* 2.9 38.0 + - + +
118M MET* 6.2 0.9 - - + -
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Residues in contact with PHE 81 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B GLU* 3.7 25.6 - - + -
298B LEU* 3.8 20.9 - - + -
301B VAL* 4.4 10.8 - - + -
48M PRO* 3.5 26.5 - - + -
49M ILE* 4.6 3.1 - - + -
58M MET* 3.9 12.8 - - + -
59M TRP 3.4 34.1 - - - -
60M ILE* 3.6 18.8 - - + -
77M VAL* 2.9 48.5 + - + +
80M VAL* 1.3 74.1 - - - +
82M SER* 1.3 64.0 + - - +
84M LEU* 3.2 7.2 + - + +
85M TYR* 3.0 32.4 + + + -
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Residues in contact with SER 82 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B TRP* 3.4 17.7 - - - -
252B ASN* 3.5 25.2 + - - -
253B SER 4.2 1.0 + - - -
254B ALA* 3.5 14.9 + - - +
298B LEU* 3.9 16.9 - - - +
78M SER 3.0 19.3 + - - -
81M PHE* 1.3 75.6 - - - +
83M PHE* 1.3 55.8 + - - +
85M TYR* 3.5 4.6 + - - +
86M LYS* 3.0 30.0 + - - +
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Residues in contact with PHE 83 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B TRP* 3.5 8.6 - + + -
3M ALA* 5.3 2.5 - - + -
6M VAL* 3.6 26.0 - - + -
21M TYR* 4.8 2.9 - - - -
79M LEU 2.9 19.7 + - - +
80M VAL* 3.6 9.2 - - + +
81M PHE 3.2 0.4 - - - -
82M SER* 1.3 75.7 - - - +
84M LEU* 1.3 65.1 + - + +
86M LYS* 3.7 1.2 - - + -
87M VAL* 2.9 52.7 + - + +
114M LEU* 5.1 1.3 - - + -
117M LEU* 4.0 22.2 - - + -
118M MET* 3.6 39.0 - - + -
123M PRO* 3.6 35.2 - - + -
126M THR* 4.5 9.4 - - + -
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Residues in contact with LEU 84 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6M VAL* 4.9 9.0 - - + -
58M MET 4.4 3.6 - - - +
59M TRP* 4.3 6.5 - - - +
60M ILE* 3.8 34.6 - - + +
67M LEU* 3.3 40.7 - - + +
69M ALA* 4.0 15.5 - - + -
80M VAL* 2.9 32.8 + - + +
81M PHE* 3.2 13.9 + - + +
83M PHE* 1.3 86.1 - - + +
85M TYR* 1.3 58.1 + - - +
87M VAL* 3.2 5.9 + - + +
88M VAL* 3.0 29.8 + - - +
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Residues in contact with TYR 85 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B GLU* 3.1 41.7 - - + +
296B PRO* 4.8 1.0 - - - +
297B GLU* 2.3 45.8 + - + +
298B LEU* 4.7 10.8 - - + -
60M ILE* 3.6 34.5 - - + +
61M LYS 6.1 1.1 - - - -
62M HIS* 6.0 3.4 - + - -
81M PHE* 3.0 32.3 + + + +
82M SER* 4.2 3.8 - - - +
84M LEU* 1.3 76.9 - - - +
86M LYS* 1.3 58.2 + - - +
88M VAL* 3.5 13.0 + - + +
89M GLN* 3.0 28.7 + - - +
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Residues in contact with LYS 86 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B GLU* 2.4 37.4 + - - -
217B TRP* 3.9 18.0 - - + -
252B ASN* 5.0 5.4 - - - +
82M SER 3.0 17.9 + - - +
83M PHE* 3.3 4.2 + - + +
84M LEU 3.2 0.2 - - - -
85M TYR* 1.3 76.6 - - - +
87M VAL* 1.3 59.0 + - - +
89M GLN* 3.7 25.7 - - + +
90M VAL* 2.9 30.0 + - + +
126M THR* 3.6 38.0 + - + +
127M ASP* 5.2 1.0 + - - +
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Residues in contact with VAL 87 (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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6M VAL* 5.4 5.4 - - + -
67M LEU* 3.6 16.6 - - + -
83M PHE* 2.9 51.1 + - + +
84M LEU* 3.5 6.3 - - + +
86M LYS* 1.3 74.5 - - - +
88M VAL* 1.3 59.9 + - - +
90M VAL* 3.3 5.7 + - - +
91M PHE* 2.9 61.2 + - + -
114M LEU* 4.7 8.5 - - + -
117M LEU* 3.8 14.4 - - + -
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Residues in contact with VAL 88 (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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60M ILE* 3.7 20.4 - - + -
62M HIS* 3.5 39.9 - - + +
67M LEU* 3.8 19.3 - - + -
84M LEU 3.0 16.1 + - - +
85M TYR* 3.6 16.6 - - + +
87M VAL* 1.3 75.4 - - - +
89M GLN* 1.3 58.6 + - - +
91M PHE* 3.5 1.3 + - - +
92M SER* 2.9 32.1 + - - +
98M LEU* 4.5 8.2 - - + +
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Residues in contact with GLN 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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85M TYR 3.0 17.6 + - - +
86M LYS* 3.8 27.9 - - + +
87M VAL 3.2 0.4 - - - -
88M VAL* 1.3 77.3 - - + +
90M VAL* 1.3 59.0 + - + +
92M SER* 3.7 4.1 - - - -
93M GLU* 2.9 50.6 + - + +
128M SER* 6.1 0.7 - - - +
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Residues in contact with VAL 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 LYS* 2.9 24.5 + - + +
87M VAL* 3.8 5.8 - - - +
89M GLN* 1.3 74.7 - - + +
91M PHE* 1.3 67.0 + - + +
93M GLU* 3.2 6.7 + - - +
94M TYR* 3.0 27.5 + - + +
113M LEU* 4.2 20.2 - - + -
117M LEU* 4.2 21.5 - - + -
126M THR 3.5 24.7 - - - +
128M SER* 4.4 13.2 - - - -
131M LEU* 4.1 19.7 - - + -
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Residues in contact with PHE 91 (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 VAL* 4.6 18.2 - - + -
65M LEU* 5.3 0.9 - - + -
67M LEU* 5.1 2.7 - - + -
87M VAL* 2.9 42.5 + - + +
88M VAL 3.9 3.1 - - - +
90M VAL* 1.3 78.6 - - + +
92M SER* 1.3 54.2 + - - +
94M TYR* 3.2 1.2 + - - +
95M PHE* 2.6 52.3 + + + +
98M LEU* 3.8 37.0 - - + -
103M ILE* 4.6 6.1 - - + -
110M ILE* 3.7 28.3 - - + -
113M LEU* 3.6 35.2 - - + -
114M LEU* 4.5 13.7 - - + -
117M LEU* 5.2 1.8 - - + -
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Residues in contact with SER 92 (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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62M HIS* 4.6 8.8 + - - -
88M VAL* 2.9 21.6 + - - +
89M GLN* 3.7 5.2 - - - -
91M PHE* 1.3 75.4 - - - +
93M GLU* 1.3 64.7 + - - +
94M TYR 3.5 0.2 - - - -
95M PHE 3.3 15.8 + - - +
96M LYS* 4.1 15.5 - - - +
97M GLU* 5.3 0.3 - - - -
98M LEU* 3.9 20.5 + - - +
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Residues in contact with GLU 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 GLN* 2.9 35.8 + - + +
90M VAL 3.2 4.6 + - - +
92M SER* 1.3 80.3 - - - +
94M TYR* 1.3 64.6 + - - +
96M LYS* 5.2 7.9 + - - -
128M SER* 3.8 27.9 + - - +
132M GLN* 3.8 18.4 + - - +
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Residues in contact with TYR 94 (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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90M VAL* 3.0 16.5 + - + +
91M PHE 3.9 1.3 - - - +
93M GLU* 1.3 86.4 - - + +
95M PHE* 1.3 80.3 + + + +
96M LYS* 3.9 19.2 + - - +
109M ILE* 3.8 26.7 - - + -
113M LEU* 3.6 39.0 - - + -
128M SER* 4.5 9.2 - - - -
131M LEU* 2.9 40.0 + - + +
132M GLN* 3.5 28.9 - - + -
135M ILE* 3.0 12.1 + - - +
137M GLN* 4.5 13.5 + - - +
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Residues in contact with PHE 95 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91M PHE* 2.6 47.2 + + + +
92M SER* 3.3 10.5 - - - -
94M TYR* 1.3 93.6 - + + +
96M LYS* 1.3 62.1 + - - +
97M GLU 3.0 23.7 + - - +
98M LEU* 4.6 4.5 - - + -
102M SER* 4.1 19.7 - - - +
103M ILE* 5.0 0.2 - - + -
106M ASN* 3.3 29.8 - - + +
109M ILE* 3.6 27.1 - - + -
110M ILE* 3.6 30.1 - - + -
113M LEU* 4.9 1.3 - - + -
137M GLN* 4.2 11.7 - - - -
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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
------------------------------------------------------------
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