Contacts of the helix formed by residues 69 - 81 (chain K) in PDB entry 5M64
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 ASP 69 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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931B TRP* 5.2 3.2 - - - -
934B ILE* 3.2 31.3 - - + +
935B ASP* 3.6 6.6 - - - +
69C ARG* 3.9 7.9 - - - +
74C GLU* 6.0 2.0 - - - +
68K GLU* 1.3 80.0 + - - +
70K HIS* 1.3 93.5 + - - +
71K THR* 3.0 19.5 + - + +
72K LEU* 3.1 4.2 + - - +
73K GLY* 2.8 21.7 + - - -
93K ILE* 5.6 0.9 - - - +
101K LEU* 3.6 15.6 - - - +
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Residues in contact with HIS 70 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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935B ASP* 3.2 26.5 + - - -
1017B ALA* 3.9 26.1 + - + +
62C SER 5.6 0.3 - - - +
66C ALA* 5.3 1.2 - - - +
69C ARG* 3.2 19.4 + - - +
69K ASP* 1.3 98.3 + - - +
71K THR* 1.3 61.1 + - - +
72K LEU 3.2 0.7 - - - -
73K GLY* 3.6 5.8 - - - +
74K ASN* 2.9 32.0 + - + +
75K ALA 3.8 0.3 + - - -
91K TYR* 3.4 41.7 + + - -
93K ILE* 3.6 26.8 - - + +
101K LEU* 6.0 0.4 - - - +
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Residues in contact with THR 71 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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934B ILE* 5.8 0.7 - - + -
66C ALA* 3.9 26.3 - - - +
69C ARG* 3.6 41.8 - - + +
70C ILE* 4.3 17.9 - - + +
74C GLU* 4.7 9.5 + - - +
321C LEU* 5.2 3.6 - - - +
68K GLU* 4.7 0.5 + - - -
69K ASP* 4.0 13.6 + - + +
70K HIS* 1.3 78.6 - - - +
72K LEU* 1.3 77.1 + - - +
75K ALA* 3.2 22.0 - - - +
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Residues in contact with LEU 72 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70C ILE* 5.8 0.7 - - + -
321C LEU* 4.3 18.8 - - + -
324C LYS* 3.7 29.6 - - + -
325C ALA* 5.6 3.4 - - - +
328C LEU* 4.5 16.8 - - + -
65K ILE* 6.3 0.4 - - + -
68K GLU* 3.3 33.9 - - + +
69K ASP 3.1 3.4 + - - +
71K THR* 1.3 98.3 + - - +
73K GLY* 1.3 59.3 + - - +
74K ASN 3.4 0.2 - - - -
75K ALA* 4.5 2.2 - - + -
76K LEU* 3.0 40.2 + - + +
121K LEU* 6.3 0.7 - - + -
124K LEU* 5.2 16.6 - - + -
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Residues in contact with GLY 73 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69K ASP 2.8 17.3 + - - -
70K HIS* 4.2 2.7 - - - -
72K LEU* 1.3 78.3 - - - +
74K ASN* 1.3 56.2 + - - +
76K LEU* 4.4 1.4 - - - +
77K ARG* 3.2 26.5 + - - +
91K TYR* 3.6 27.3 - - - +
101K LEU* 5.4 5.4 - - - -
103K ILE* 5.1 9.0 - - - +
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Residues in contact with ASN 74 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1017B ALA 4.0 8.8 + - - +
1018B THR* 3.3 29.5 + - - +
62C SER* 3.5 27.6 + - - +
65C ASN* 5.8 1.8 - - - +
70K HIS* 2.9 28.2 + - + +
73K GLY* 1.3 74.4 - - - +
75K ALA* 1.3 59.8 + - - +
77K ARG* 3.3 8.2 + - - +
78K TYR* 3.0 28.4 + - - +
91K TYR* 4.5 16.4 - - + +
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Residues in contact with ALA 75 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62C SER* 4.4 6.2 + - - +
63C ILE* 3.8 28.0 - - + +
66C ALA* 4.7 7.9 - - + -
321C LEU* 6.4 0.9 - - + -
70K HIS 3.8 2.8 + - - -
71K THR 3.2 21.3 - - - +
72K LEU* 3.9 3.8 + - + +
73K GLY 3.5 0.2 - - - -
74K ASN* 1.3 79.2 - - - +
76K LEU* 1.3 63.0 + - - +
78K TYR* 3.3 3.3 + - - +
79K VAL* 3.1 26.5 + - - +
124K LEU* 4.7 12.7 - - + +
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Residues in contact with LEU 76 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328C LEU* 6.1 3.6 - - + -
72K LEU* 3.0 26.6 + - + +
73K GLY* 4.4 2.0 - - - +
75K ALA* 1.3 76.7 - - - +
77K ARG* 1.3 57.4 + - - +
79K VAL* 3.6 5.2 - - + -
80K ILE* 2.8 59.1 + - + +
89K CYS* 5.7 0.4 - - - -
103K ILE* 4.6 25.8 - - + -
105K ILE* 6.1 1.1 - - + -
117K LEU* 3.9 27.4 - - + -
120K GLY 4.7 2.0 - - - -
121K LEU* 4.4 11.2 - - + -
124K LEU* 3.9 23.5 - - + +
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Residues in contact with ARG 77 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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689A ARG* 5.0 2.6 - - - +
690A GLU* 2.7 44.4 + - + +
693A GLN* 3.2 24.4 + - - +
694A GLN* 4.8 7.1 - - + +
73K GLY 3.2 21.3 + - - +
74K ASN* 3.5 10.1 - - - +
75K ALA 3.2 0.4 - - - -
76K LEU* 1.3 77.8 - - - +
78K TYR* 1.3 61.0 + - - +
81K MET* 3.2 49.4 + - - +
86K VAL* 5.1 1.0 - - - +
89K CYS* 3.0 45.1 + - - +
90K GLY* 3.6 24.2 - - - -
91K TYR* 4.2 15.5 - - + +
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Residues in contact with TYR 78 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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690A GLU* 5.3 4.0 - - + -
31C TRP* 4.9 5.0 - - - -
60C ASP* 3.2 43.1 + - + +
62C SER* 3.3 26.0 - - - +
63C ILE* 4.7 11.4 - - + -
74K ASN* 3.0 15.2 + - - +
75K ALA 3.3 2.9 + - - +
77K ARG* 1.3 78.4 - - - +
79K VAL* 1.3 60.1 + - + +
81K MET* 3.2 42.1 - - + +
82K LYS* 3.2 37.9 + - - +
127K LEU* 6.3 0.9 - - + -
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Residues in contact with VAL 79 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C TRP* 6.1 2.7 - - + +
63C ILE* 5.9 1.1 - - + -
75K ALA 3.1 20.3 + - - +
76K LEU* 3.4 11.4 - - + +
78K TYR* 1.3 83.3 - - + +
80K ILE* 1.3 69.0 + - + +
81K MET 3.4 0.4 - - - -
82K LYS* 3.6 21.1 + - + +
83K ASN* 4.3 2.3 + - - +
120K GLY* 4.5 4.0 - - - +
123K ASP* 3.6 39.9 - - + +
124K LEU* 3.6 28.7 - - + -
127K LEU* 5.3 12.6 - - + -
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Residues in contact with ILE 80 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76K LEU* 2.8 41.3 + - + +
77K ARG 4.3 1.8 - - - +
79K VAL* 1.3 74.8 - - - +
81K MET* 1.3 65.7 + - - +
82K LYS 3.1 0.7 - - - -
83K ASN* 3.0 26.9 + - + +
86K VAL* 3.9 17.0 - - + +
89K CYS* 3.8 30.3 - - + -
105K ILE* 4.4 11.9 - - + -
116K ALA* 3.6 29.2 - - + +
117K LEU* 4.4 8.3 - - + -
120K GLY* 3.7 19.1 - - - -
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Residues in contact with MET 81 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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689A ARG* 4.2 15.5 + - - +
690A GLU* 3.2 47.1 - - + +
77K ARG* 3.2 26.4 + - - +
78K TYR* 3.2 51.4 - - + +
80K ILE* 1.3 78.1 - - - +
82K LYS* 1.3 76.5 + - + +
83K ASN 3.1 8.9 + - - +
86K VAL* 5.2 3.7 - - - +
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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
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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