Contacts of the helix formed by residues 82 - 94 (chain C) in PDB entry 6FQS
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 GLY 82 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122A ARG* 4.0 20.5 - - - +
81C HIS* 1.3 80.3 - - - +
83C ASP* 1.3 70.7 + - - -
84C SER* 3.2 5.3 + - - -
85C SER* 3.3 20.1 + - - -
86C ILE* 3.6 8.8 + - - +
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Residues in contact with ASP 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A ARG* 3.7 18.5 + - - -
71C VAL* 4.1 21.4 - - + +
75C MET* 4.4 17.0 - - + +
81C HIS 3.7 1.9 + - - -
82C GLY* 1.3 70.2 - - - -
84C SER* 1.3 54.1 + - - -
86C ILE* 3.1 4.6 + - - +
87C TYR* 2.7 36.8 + - - +
121C MET* 4.2 17.9 - - + +
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Residues in contact with SER 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C GLY* 4.6 2.6 + - - -
83C ASP* 1.3 81.5 + - - +
85C SER* 1.3 70.6 + - - +
87C TYR* 4.5 4.5 - - - +
88C GLU* 2.8 47.7 + - - +
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Residues in contact with SER 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C VAL* 4.5 4.1 - - - +
79C HIS* 5.2 5.6 - - - -
81C HIS* 4.9 8.7 - - - +
82C GLY* 3.5 15.8 + - - -
83C ASP 3.2 0.4 - - - -
84C SER* 1.3 81.4 + - - +
86C ILE* 1.3 64.9 + - - +
88C GLU* 4.1 2.7 - - - +
89C ALA* 3.1 25.3 + - - +
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Residues in contact with ILE 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C VAL* 4.1 10.1 - - + -
49C ILE* 3.5 22.6 - - + +
71C VAL* 3.6 29.8 - - + -
74C VAL* 4.5 7.4 - - + -
75C MET* 3.7 37.9 - - + +
79C HIS* 3.5 37.2 - - + -
81C HIS 4.2 3.1 - - - +
82C GLY 3.6 12.3 + - - +
83C ASP 3.1 6.3 + - - +
85C SER* 1.3 76.3 - - - +
87C TYR* 1.3 66.3 + - - +
89C ALA 3.3 0.7 + - - -
90C MET* 3.0 20.4 + - + +
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Residues in contact with TYR 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C SER* 3.8 12.8 - - - -
71C VAL* 4.1 10.7 - - + +
83C ASP 2.7 20.6 + - - +
84C SER* 4.2 3.6 - - - +
86C ILE* 1.3 74.1 - - - +
88C GLU* 1.3 65.8 + - + +
90C MET* 3.2 13.9 + - + +
91C VAL* 2.9 55.5 + - + +
110C PHE* 4.7 1.2 - + - -
118C ALA* 4.2 7.3 - - + +
119C ALA 2.5 29.7 + - - -
120C ALA* 3.9 1.3 + - - -
121C MET* 3.2 42.0 - - + -
124C THR* 3.3 33.2 + - - +
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Residues in contact with GLU 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C SER* 2.8 38.6 + - - +
85C SER* 4.1 2.9 - - - +
87C TYR* 1.3 80.8 - - + +
89C ALA* 1.3 66.1 - - - +
91C VAL* 3.3 8.7 + - - +
92C ARG* 3.1 26.6 + - - +
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Residues in contact with ALA 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C VAL* 4.1 14.8 - - + -
46C HIS* 4.0 21.2 - - - +
49C ILE* 3.8 13.9 - - + -
85C SER 3.1 19.6 + - - +
86C ILE 3.7 3.6 - - - +
88C GLU* 1.3 78.6 - - - +
90C MET* 1.3 60.8 + - - +
92C ARG* 3.4 9.0 + - - +
93C MET* 3.3 26.5 + - - +
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Residues in contact with MET 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C ILE* 3.8 22.1 - - + +
53C LEU* 5.3 2.5 - - - -
67C SER* 3.9 28.5 - - - +
70C ILE* 4.1 25.6 - - - -
71C VAL* 5.0 4.9 - - + -
86C ILE* 3.0 15.8 + - + +
87C TYR* 3.5 21.8 - - + +
89C ALA* 1.3 77.4 - - - +
91C VAL* 1.3 61.3 + - - +
93C MET* 3.2 21.2 + - - +
94C ALA* 3.4 11.3 + - - +
104C VAL* 4.1 15.8 - - + +
110C PHE* 4.4 10.3 - - + -
126C ALA* 3.7 28.3 - - + -
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Residues in contact with VAL 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87C TYR* 2.9 55.1 + - + +
88C GLU* 3.6 9.2 - - - +
89C ALA 3.3 0.2 - - - -
90C MET* 1.3 75.5 - - + +
92C ARG* 1.3 58.0 + - + +
94C ALA* 2.8 23.9 + - - +
95C GLN* 3.4 17.2 - - - +
110C PHE* 3.3 45.5 - - + +
118C ALA* 3.8 12.8 - - + +
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Residues in contact with ARG 92 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43C LYS* 5.6 4.8 - - - +
46C HIS* 4.7 11.1 + - - +
88C GLU 3.1 12.1 + - - +
89C ALA* 3.5 13.0 - - - +
91C VAL* 1.3 77.4 - - - +
93C MET* 1.3 61.7 + - + +
94C ALA 3.1 1.4 + - - -
95C GLN* 3.2 24.0 + - - +
98C SER* 3.7 32.0 + - - -
99C TYR* 3.2 51.0 + - + -
170C ASN 5.7 2.8 + - - -
172C ALA* 6.4 0.8 - - - +
173C SER* 5.6 12.4 + - - +
266C PHE* 5.3 4.2 - - - -
267C GLN* 5.0 11.1 - - - +
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Residues in contact with MET 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C HIS* 3.5 28.7 - - + +
49C ILE* 3.7 35.0 - - + -
50C LEU* 4.6 6.1 - - + -
89C ALA 3.3 8.5 + - - +
90C MET* 3.2 28.4 + - - +
91C VAL 3.2 1.2 - - - -
92C ARG* 1.3 78.3 - - - +
94C ALA* 1.3 57.3 + - - +
95C GLN 3.5 0.4 - - - -
99C TYR* 3.5 34.7 - - + +
102C PRO* 3.6 8.1 - - - +
103C LEU* 3.3 32.1 + - + -
104C VAL* 3.2 31.6 + - + +
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Residues in contact with ALA 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C MET 3.4 4.3 + - - +
91C VAL 2.8 12.3 + - - +
93C MET* 1.3 78.7 - - - +
95C GLN* 1.3 59.6 + - - +
96C ASP* 3.9 3.5 + - - +
102C PRO* 4.9 4.0 - - - +
104C VAL* 3.2 36.9 - - + +
106C GLY 4.4 8.2 + - - +
110C PHE* 3.9 26.4 - - + +
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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