Contacts of the helix formed by residues 72 - 90 (chain M) in PDB entry 6K4Y
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 THR 72 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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589F GLN* 6.2 2.2 - - + -
592F ALA* 6.0 5.8 - - + -
593F LYS* 5.4 6.1 - - - +
60M GLY 3.9 10.6 + - - +
61M LEU* 2.9 34.4 + - - +
63M GLU* 5.0 17.3 - - + +
71M ILE* 1.3 80.3 - - - +
73M GLY* 1.3 61.5 + - - +
74M GLU* 3.0 19.8 + - - -
75M ALA* 3.5 1.8 + - - +
76M GLN* 3.0 26.5 + - - +
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Residues in contact with GLY 73 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592F ALA* 4.3 13.4 + - - +
593F LYS* 5.0 2.2 - - - -
596F ARG* 3.3 26.3 - - - +
72M THR* 1.3 75.1 - - - +
74M GLU* 1.3 64.5 + - - +
76M GLN* 3.3 9.2 - - - +
77M ASP* 2.9 32.9 + - - +
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Residues in contact with GLU 74 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596F ARG* 6.2 1.6 - - - -
61M LEU* 4.7 8.9 - - + +
72M THR* 3.0 21.8 + - - +
73M GLY* 1.3 74.4 + - - +
75M ALA* 1.3 60.2 + - - +
77M ASP* 3.0 15.2 + - - +
78M ILE* 3.0 32.2 + - + +
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Residues in contact with ALA 75 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23M LEU* 5.0 8.1 - - + -
61M LEU* 3.8 38.8 - - + +
71M ILE* 4.0 19.3 - - + -
72M THR 3.5 8.4 + - - +
74M GLU* 1.3 77.3 - - - +
76M GLN* 1.3 58.1 + - - +
78M ILE* 3.1 16.0 + - + +
79M ILE* 2.9 32.1 + - - +
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Residues in contact with GLN 76 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593F LYS* 3.4 38.3 - - + +
596F ARG* 4.9 9.6 - - + -
597F LYS* 2.8 39.9 + - + +
27M ALA* 5.6 2.2 - - - +
71M ILE* 3.7 17.8 - - + +
72M THR 3.0 16.9 + - - +
73M GLY* 3.3 15.7 - - - +
74M GLU 3.2 0.2 - - - -
75M ALA* 1.3 76.2 - - - +
77M ASP* 1.3 56.7 + - - +
79M ILE* 3.2 14.9 + - - +
80M SER* 2.9 29.3 + - - -
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Residues in contact with ASP 77 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596F ARG* 3.3 34.1 + - - +
599F ARG* 3.1 34.8 + - - +
600F HIS* 4.3 9.4 + - - +
73M GLY 2.9 19.1 + - - +
74M GLU* 3.0 14.8 + - - +
76M GLN* 1.3 74.0 - - - +
78M ILE* 1.3 58.2 + - + +
80M SER* 4.1 5.0 - - - +
81M ASN* 2.7 44.3 + - - +
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Residues in contact with ILE 78 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7M ILE* 4.1 8.1 - - + +
10M ALA* 3.6 36.3 - - + +
11M SER* 3.8 21.8 - - - +
14M VAL* 6.3 0.9 - - + -
23M LEU* 5.6 5.4 - - + -
61M LEU* 4.7 14.4 - - + -
74M GLU* 3.0 16.5 + - + +
75M ALA* 3.1 19.7 + - + +
77M ASP* 1.3 78.9 - - + +
79M ILE* 1.3 61.2 + - + +
81M ASN* 3.5 6.8 + - - +
82M ALA* 2.9 27.2 + - - +
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Residues in contact with ILE 79 (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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607F LEU 6.0 1.6 - - - +
610F PHE* 5.5 12.9 - - + -
7M ILE* 3.7 25.8 - - + -
23M LEU* 4.4 23.1 - - + +
24M ILE* 4.5 11.2 - - + -
27M ALA* 4.6 22.0 - - + -
71M ILE* 4.6 3.1 - - + -
75M ALA 2.9 21.4 + - - +
76M GLN* 3.6 17.9 - - - +
78M ILE* 1.3 79.5 - - + +
80M SER* 1.3 58.5 + - - +
82M ALA* 3.0 5.5 + - + +
83M ALA* 2.9 28.3 + - + +
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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
----------------------------------------------------------
597F LYS* 4.9 9.0 - - - -
600F HIS* 3.1 38.7 - - - +
602F SER* 5.3 0.7 + - - -
607F LEU* 5.2 13.0 - - - +
76M GLN* 2.9 21.0 + - - -
77M ASP* 4.1 3.1 - - - -
78M ILE 3.4 0.2 - - - -
79M ILE* 1.3 74.8 - - - +
81M ASN* 1.3 56.4 + - - +
83M ALA* 3.6 6.6 + - - +
84M THR* 2.3 38.4 + - - -
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Residues in contact with ASN 81 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599F ARG* 5.4 2.6 - - - +
600F HIS* 3.5 22.6 + - - -
10M ALA* 4.5 12.7 + - + +
77M ASP* 2.7 33.8 + - - +
78M ILE* 3.8 6.8 - - - +
80M SER* 1.3 75.5 - - - +
82M ALA* 1.3 59.0 + - - +
84M THR* 3.3 8.8 + - - +
85M LEU* 2.9 37.8 + - + +
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Residues in contact with ALA 82 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610F PHE* 4.4 5.8 - - + -
6M TYR* 3.5 41.2 - - + +
7M ILE* 3.7 21.3 - - + -
10M ALA* 4.2 0.4 - - - +
78M ILE 2.9 15.8 + - - +
79M ILE* 3.0 9.6 + - + +
81M ASN* 1.3 77.4 - - - +
83M ALA* 1.3 57.3 + - - +
85M LEU* 3.6 1.1 + - - -
86M TYR* 2.9 28.3 + - - +
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Residues in contact with ALA 83 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606F VAL* 3.3 38.9 - - + +
607F LEU* 4.7 8.1 - - + +
610F PHE* 3.6 22.3 - - + -
79M ILE* 2.9 16.0 + - + +
80M SER* 4.1 6.3 - - - +
82M ALA* 1.3 72.9 - - - +
84M THR* 1.3 60.6 + - - +
86M TYR* 3.7 0.8 - - - +
87M ALA* 2.9 26.9 + - - +
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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
----------------------------------------------------------
600F HIS* 4.5 12.1 + - - +
606F VAL* 6.2 0.7 - - - -
80M SER* 2.3 30.7 + - - -
81M ASN* 3.2 14.6 + - - +
83M ALA* 1.3 78.9 - - - +
85M LEU* 1.3 61.3 + - + +
87M ALA* 3.1 8.6 + - - +
88M GLN* 2.9 45.2 + - + +
95M LEU* 5.1 5.7 - - + +
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Residues in contact with LEU 85 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6M TYR* 3.5 22.4 - - + +
9M LYS* 3.4 41.1 - - + +
10M ALA* 5.1 9.4 - - + -
81M ASN* 2.9 24.3 + - + +
82M ALA* 5.1 0.4 - - - -
84M THR* 1.3 76.3 - - + +
86M TYR* 1.3 60.3 + - - +
88M GLN* 3.0 32.2 + - - +
89M GLU* 2.9 39.1 + - - +
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Residues in contact with TYR 86 (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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606F VAL* 4.6 6.3 - - + -
609F SER* 3.8 27.6 + - - -
610F PHE* 3.4 34.8 - + + -
3M LYS* 4.3 26.4 + - + -
6M TYR* 3.5 15.4 - + + -
82M ALA 2.9 19.9 + - - +
83M ALA* 3.7 7.0 - - - +
85M LEU* 1.3 77.2 - - - +
87M ALA* 1.3 57.4 + - - +
90M ASN* 2.9 74.2 + - + +
91M ALA* 3.2 10.6 + - + -
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Residues in contact with ALA 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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606F VAL* 3.7 18.8 - - + -
83M ALA 2.9 18.5 + - - +
84M THR* 3.1 8.0 + - + +
86M TYR* 1.3 76.1 - - - +
88M GLN* 1.3 63.8 + - - +
89M GLU 3.2 0.4 - - - -
91M ALA* 2.9 38.6 - - + +
92M PRO* 3.4 6.2 - - - +
94M LEU* 5.9 0.2 - - + -
95M LEU* 4.3 24.4 - - + +
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Residues in contact with GLN 88 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84M THR* 2.9 28.0 + - - +
85M LEU* 3.0 36.3 + - - +
87M ALA* 1.3 77.8 - - - +
89M GLU* 1.3 65.8 + - + +
92M PRO* 4.8 9.5 - - - +
95M LEU* 4.5 15.7 - - + +
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Residues in contact with GLU 89 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6M TYR* 2.7 40.1 + - - +
85M LEU* 2.9 14.3 + - - +
88M GLN* 1.3 88.1 - - + +
90M ASN* 1.3 63.2 + - - +
92M PRO* 4.9 6.4 - - - +
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Residues in contact with ASN 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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3M LYS* 5.4 4.4 - - - +
6M TYR* 2.3 38.0 + - - -
86M TYR* 2.9 44.7 + - + +
88M GLN 3.8 0.2 - - - -
89M GLU* 1.3 82.4 + - - +
91M ALA* 1.3 58.8 + - - +
92M PRO* 3.5 10.5 - - - +
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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