Contacts of the helix formed by residues 91 - 103 (chain H) in PDB entry 6R93
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 91 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45G GLY* 5.1 7.9 - - - -
48G ALA* 4.1 7.0 - - - -
87H ARG* 4.1 13.2 + - - +
89H THR* 3.8 20.4 - - - +
90H ILE* 1.3 78.3 - - - +
92H SER* 1.3 66.5 + - - +
93H ARG* 3.1 18.4 + - - +
94H GLU* 2.6 35.0 + - - +
95H ILE* 3.4 14.4 + - - +
111I T 6.1 0.4 - - - +
39J G 6.0 3.1 - - - -
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Residues in contact with SER 92 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47G GLY* 4.2 20.8 - - - +
48G ALA* 4.2 12.5 - - - +
51G TYR* 4.1 22.3 - - - -
91H THR* 1.3 75.8 - - - +
93H ARG* 1.3 62.8 + - - +
95H ILE* 3.4 5.8 + - - +
96H GLN* 2.9 29.4 + - - +
119H VAL* 5.3 10.0 - - - +
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Residues in contact with ARG 93 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75F GLU 4.6 4.0 + - - -
76F HIS* 3.9 17.1 + - + +
78F LYS* 3.7 41.2 - - - +
87H ARG* 3.3 34.0 - - - +
91H THR* 3.0 13.7 - - - +
92H SER* 1.3 80.3 + - - +
94H GLU* 1.3 64.9 + - - +
96H GLN* 3.2 10.2 + - - +
97H THR* 2.9 32.9 + - - +
40J G 4.6 14.4 + - - -
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Residues in contact with GLU 94 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76F HIS* 3.1 29.6 + - + +
78H ALA* 4.2 22.6 - - + +
81H LEU* 4.7 7.7 - - + +
82H ALA* 4.8 5.9 - - + +
87H ARG* 3.0 35.0 + - - +
89H THR 3.7 7.9 - - - +
90H ILE* 4.2 17.0 - - + -
91H THR* 2.6 33.7 + - - +
93H ARG* 1.3 71.4 - - - +
95H ILE* 1.3 67.6 + - - +
97H THR* 3.4 1.8 + - - -
98H ALA* 2.9 26.0 + - - +
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Residues in contact with ILE 95 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35G LEU* 5.7 3.6 - - + -
48G ALA* 3.8 25.8 - - + +
51G TYR* 3.7 25.1 - - + -
52G LEU* 4.2 25.8 - - + +
74H ILE* 4.4 20.2 - - + -
75H ALA* 5.8 0.9 - - - -
78H ALA* 4.4 3.4 - - + -
90H ILE* 3.9 25.1 - - + -
91H THR 3.5 12.1 - - - +
92H SER* 3.7 7.4 - - - +
93H ARG 3.3 0.6 - - - -
94H GLU* 1.3 78.4 - - - +
96H GLN* 1.3 55.8 + - - +
98H ALA* 3.3 4.4 + - - +
99H VAL* 2.9 42.7 + - + +
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Residues in contact with GLN 96 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51G TYR* 2.7 45.0 + - - +
92H SER 2.9 17.8 + - - +
93H ARG* 3.4 9.2 - - - +
95H ILE* 1.3 76.2 - - - +
97H THR* 1.3 64.3 + - - +
99H VAL* 3.2 4.9 + - - +
100H ARG* 3.0 57.1 + - - +
112H VAL* 4.3 10.4 - - + +
116H THR* 4.1 9.3 + - - -
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Residues in contact with THR 97 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72F THR* 3.5 26.2 - - + +
73F TYR 5.3 0.4 - - - +
76F HIS* 3.3 28.9 + - + +
81H LEU* 3.4 24.5 - - + -
93H ARG* 2.9 17.0 + - - +
94H GLU 3.8 3.8 - - - -
96H GLN* 1.3 77.6 - - - +
98H ALA* 1.3 63.3 + - - +
100H ARG* 3.1 16.1 + - - +
101H LEU* 2.9 25.7 + - + +
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Residues in contact with ALA 98 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74H ILE* 4.3 23.8 - - + +
77H GLU* 3.9 32.5 - - + +
78H ALA* 4.4 4.9 - - - +
81H LEU* 4.9 2.1 - - + +
94H GLU 2.9 17.4 + - - +
95H ILE* 3.6 4.3 - - - +
97H THR* 1.3 75.8 - - - +
99H VAL* 1.3 56.7 + - - +
101H LEU* 3.2 5.1 + - - +
102H LEU* 2.9 33.4 + - - +
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Residues in contact with VAL 99 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51G TYR* 4.6 2.2 - - + -
52G LEU* 6.0 0.2 - - + -
55G VAL* 4.2 30.3 - - + -
74H ILE* 4.7 15.3 - - + -
95H ILE* 2.9 31.4 + - + +
96H GLN* 3.5 5.4 - - - +
98H ALA* 1.3 75.2 - - - +
100H ARG* 1.3 63.1 + - - +
102H LEU* 5.0 2.2 - - - -
103H LEU* 3.0 46.3 + - + +
108H ALA* 4.3 7.5 - - - +
111H ALA* 4.7 1.1 - - + -
112H VAL* 3.6 24.7 - - + -
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Residues in contact with ARG 100 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68F ARG* 5.8 3.5 - - - -
72F THR* 4.7 19.7 - - + +
75F GLU* 4.0 20.9 + - - +
96H GLN* 3.0 47.5 + - - +
97H THR* 3.1 17.0 + - - +
99H VAL* 1.3 76.4 - - - +
101H LEU* 1.3 63.0 + - - +
103H LEU 3.4 12.0 - - - +
108H ALA* 4.7 10.2 - - + +
109H LYS* 4.3 21.0 - - - +
112H VAL* 4.7 16.3 - - + +
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Residues in contact with LEU 101 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69F ASP* 3.6 45.8 - - + +
72F THR* 3.8 17.9 - - + +
73F TYR* 3.5 36.6 - - + +
93F ARG* 2.7 37.8 + - - +
77H GLU* 3.9 14.6 - - + +
81H LEU* 4.4 3.1 - - + -
97H THR* 2.9 28.9 + - + +
98H ALA* 3.6 5.2 - - - +
100H ARG* 1.3 80.3 - - - +
102H LEU* 1.3 60.7 + - - +
103H LEU 4.4 1.2 - - - +
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Residues in contact with LEU 102 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93F ARG* 4.2 17.6 + - - +
97G LEU* 4.2 12.0 - - + +
70H ILE* 5.4 5.2 - - + -
73H ARG* 3.9 52.9 - - + +
74H ILE* 4.3 16.4 - - + +
77H GLU* 6.1 4.7 - - + -
98H ALA* 2.9 16.8 + - + +
99H VAL* 5.0 0.4 - - - -
101H LEU* 1.3 79.1 - - - +
103H LEU* 1.3 80.2 + - + +
104H PRO* 3.9 3.3 - - - +
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Residues in contact with LEU 103 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55G VAL* 4.4 9.0 - - + -
59G LEU* 4.2 32.5 - - + -
97G LEU* 4.3 13.9 - - + -
70H ILE* 5.7 5.8 - - + -
74H ILE* 5.7 4.3 - - + -
99H VAL* 3.0 34.0 + - + +
100H ARG 3.4 16.8 - - - +
101H LEU 4.4 1.3 - - - +
102H LEU* 1.3 105.0 - - + +
104H PRO* 1.3 70.7 - - + +
107H LEU* 4.5 9.0 - - + -
108H ALA* 3.8 18.6 - - + +
111H ALA* 4.6 7.2 - - + -
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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