Contacts of the helix formed by residues 87 - 99 (chain H) in PDB entry 5CP6
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 87 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47G ALA* 3.6 6.1 - - - -
201G SO4 3.2 27.4 - - - +
85H THR* 4.2 18.8 - - + +
86H ILE* 1.3 75.4 - - - +
88H SER* 1.3 58.5 + - - +
89H ARG* 3.0 20.6 + - - +
90H GLU* 2.5 42.0 + - - +
91H ILE* 3.2 12.6 + - - +
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Residues in contact with SER 88 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46G GLY* 4.1 6.1 - - - -
47G ALA* 3.7 15.4 - - - +
50G TYR* 3.9 23.7 - - - -
201G SO4 2.8 30.9 + - - -
87H THR* 1.3 73.3 - - - +
89H ARG* 1.3 59.1 + - - +
90H GLU 3.3 0.2 - - - -
91H ILE* 3.8 6.8 - - - +
92H GLN* 2.9 29.5 + - - +
115H VAL* 4.7 8.0 - - - +
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Residues in contact with ARG 89 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74F GLU 3.5 8.9 + - - -
75F HIS* 2.6 63.9 + - + +
77F LYS* 3.9 33.5 - - - +
87H THR* 3.0 12.9 + - - +
88H SER* 1.3 81.3 + - - +
90H GLU* 1.3 70.9 + - - +
92H GLN* 3.2 10.7 + - - +
93H THR* 3.0 28.9 + - - +
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Residues in contact with GLU 90 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75F HIS* 2.8 36.7 + - + +
74H ALA* 4.1 29.3 - - + +
77H LEU* 3.5 12.5 - - + +
78H ALA* 4.5 9.4 - - + +
83H ARG* 5.7 5.1 - - - +
85H THR 3.4 14.2 - - - +
86H ILE* 4.3 2.9 - - + -
87H THR* 2.5 49.3 + - - +
89H ARG* 1.3 87.4 + - - +
91H ILE* 1.3 52.6 + - - +
93H THR 3.4 0.5 + - - -
94H ALA* 2.8 35.1 + - - +
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Residues in contact with ILE 91 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34G LEU* 5.1 6.5 - - + -
47G ALA* 3.9 22.4 - - + +
50G TYR* 3.7 23.1 - - + -
51G LEU* 4.2 29.8 - - + +
70H ILE* 4.1 20.2 - - + -
71H ALA* 5.3 0.9 - - - -
74H ALA* 4.2 9.9 - - + -
86H ILE* 4.0 19.3 - - + -
87H THR 3.2 12.3 + - - +
88H SER* 3.8 8.1 - - - +
90H GLU* 1.3 76.9 - - - +
92H GLN* 1.3 58.7 + - - +
94H ALA* 3.4 5.3 - - - +
95H VAL* 2.9 30.5 + - + +
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Residues in contact with GLN 92 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50G TYR* 2.4 41.5 + - + +
88H SER 2.9 19.3 + - - +
89H ARG* 3.6 11.7 - - - +
90H GLU 3.2 0.2 - - - -
91H ILE* 1.3 75.7 - - - +
93H THR* 1.3 67.2 + - - +
95H VAL* 3.1 5.0 + - - +
96H ARG* 3.0 49.2 + - - +
108H VAL* 3.3 20.6 - - + +
112H THR* 3.3 12.1 + - - -
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Residues in contact with THR 93 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71F THR* 3.6 27.4 - - + +
75F HIS* 2.5 38.2 + - + +
77H LEU* 3.5 24.7 - - + -
89H ARG* 3.0 10.1 + - - +
92H GLN* 1.3 77.9 - - - +
94H ALA* 1.3 63.3 + - - +
96H ARG* 3.1 10.7 + - - +
97H LEU* 3.0 27.5 + - + +
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Residues in contact with ALA 94 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70H ILE* 3.7 28.7 - - + +
73H GLU* 4.0 14.8 - - + -
74H ALA* 4.0 10.3 - - - +
77H LEU* 3.9 2.4 - - - +
90H GLU 2.8 19.5 + - - +
91H ILE* 3.4 10.5 - - - +
93H THR* 1.3 76.9 - - - +
95H VAL* 1.3 64.0 + - - +
97H LEU* 3.1 5.8 + - - +
98H LEU* 3.0 27.2 + - - +
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Residues in contact with VAL 95 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50G TYR* 4.6 2.2 - - + -
54G VAL* 4.0 32.8 - - + -
70H ILE* 4.2 15.3 - - + -
91H ILE* 2.9 25.1 + - + +
92H GLN* 3.1 7.6 + - - +
94H ALA* 1.3 77.4 - - - +
96H ARG* 1.3 64.9 + - - +
98H LEU* 3.1 2.6 + - - -
99H LEU* 2.9 46.7 + - + +
104H ALA* 4.1 10.0 - - - +
107H ALA* 4.1 5.8 - - + -
108H VAL* 4.0 21.8 - - + +
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Residues in contact with ARG 96 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67F ARG* 5.9 2.8 - - - -
68F ASP* 5.5 0.2 - - - +
71F THR* 4.7 15.0 - - + +
92H GLN* 3.0 43.5 + - - +
93H THR* 3.1 11.9 + - - +
95H VAL* 1.3 78.5 - - - +
97H LEU* 1.3 63.9 + - - +
98H LEU 3.3 0.2 + - - -
99H LEU 3.5 13.5 - - - +
104H ALA* 4.6 10.5 - - + +
108H VAL* 4.0 34.9 - - + +
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Residues in contact with LEU 97 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68F ASP* 3.6 38.0 - - + +
71F THR* 3.8 25.4 - - + +
72F TYR* 3.9 28.9 - - + +
92F ARG* 3.1 39.4 + - - +
73H GLU* 4.0 18.2 - - + +
77H LEU* 4.5 2.9 - - + -
93H THR* 3.0 31.7 + - + +
94H ALA 3.1 6.9 + - - +
96H ARG* 1.3 77.5 - - - +
98H LEU* 1.3 59.0 + - - +
99H LEU 4.9 0.6 - - - +
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Residues in contact with LEU 98 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92F ARG* 3.5 20.9 - - - +
95G LYS* 5.5 2.6 + - - -
96G LEU* 3.8 15.2 - - + +
66H VAL* 6.0 0.2 - - + -
69H ARG* 3.4 61.7 - - + +
70H ILE* 3.4 22.0 - - + +
73H GLU* 4.4 8.7 - - + +
94H ALA 3.0 16.1 + - - +
95H VAL* 3.9 3.1 - - - +
97H LEU* 1.3 78.0 - - - +
99H LEU* 1.3 73.0 + - + +
100H PRO* 4.0 1.9 - - - +
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Residues in contact with LEU 99 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54G VAL* 5.0 2.5 - - + -
58G LEU* 4.1 26.9 - - + -
95G LYS* 5.5 1.1 - - - -
96G LEU* 3.7 28.7 - - + -
66H VAL* 5.5 5.4 - - + -
70H ILE* 5.6 3.1 - - + -
95H VAL* 2.9 26.7 + - + +
96H ARG 3.5 14.0 - - - +
97H LEU 4.9 0.5 - - - +
98H LEU* 1.3 90.7 - - + +
100H PRO* 1.3 71.2 - - + +
101H GLY 3.7 0.9 + - - -
103H LEU* 4.0 9.6 - - + +
104H ALA* 3.7 16.9 - - - +
107H ALA* 3.9 28.7 - - + -
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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