Contacts of the helix formed by residues 86 - 94 (chain A) in PDB entry 3F7G
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 SER 86 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83A GLY 4.0 1.7 + - - -
84A MET 3.2 1.4 - - - +
85A GLY* 1.3 75.0 - - - +
87A GLU* 1.3 58.4 + - - +
88A GLU* 3.4 13.5 + - - +
89A LEU* 3.1 34.9 + - - +
90A ARG* 2.9 29.0 + - - +
95C TYR* 5.2 3.1 + - - -
116C THR 4.0 15.3 + - - -
117C GLY* 5.7 2.0 - - - -
118C HIS* 6.2 3.2 - - - -
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Residues in contact with GLU 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A GLY 3.6 1.4 + - - -
86A SER* 1.3 71.0 + - - +
88A GLU* 1.3 57.6 + - - +
90A ARG* 3.1 25.3 + - - +
91A LEU* 2.8 36.2 + - + +
106A GLU* 4.5 3.1 - - - +
109A ALA* 3.8 18.7 - - + +
110A ALA* 3.7 30.5 + - - +
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Residues in contact with GLU 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A SER* 3.2 11.1 + - - +
87A GLU* 1.3 79.2 - - - +
89A LEU* 1.3 64.2 + - + +
91A LEU* 3.4 17.1 + - - +
92A ALA* 3.2 19.1 + - - +
84C MET* 4.8 3.4 - - + +
89C LEU 5.8 0.4 - - - +
92C ALA* 3.2 32.7 - - - +
93C SER* 4.2 17.0 - - - -
95C TYR* 3.8 29.2 - - + +
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Residues in contact with LEU 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A GLY 3.5 24.0 - - - +
84A MET* 3.9 8.1 - - - +
86A SER* 3.1 19.1 + - - +
88A GLU* 1.3 75.2 - - + +
90A ARG* 1.3 66.8 + - - +
92A ALA* 3.2 10.4 + - - -
93A SER 3.4 2.4 + - - -
81C PHE* 3.2 33.2 - - + -
84C MET* 3.4 27.1 - - + -
93C SER* 4.8 4.0 - - - -
114C PHE* 3.8 32.3 - - + -
115C HIS 3.9 8.5 - - - +
116C THR* 3.9 21.3 - - + +
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Residues in contact with ARG 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A MET* 3.0 38.2 + - - +
85A GLY 3.0 28.3 + - - -
86A SER 2.9 8.8 + - - +
87A GLU* 3.1 30.5 + - - +
89A LEU* 1.3 75.5 - - - +
91A LEU* 1.3 59.6 + - - +
93A SER* 2.6 24.9 + - - -
94A PHE* 3.1 11.2 - - - -
109A ALA* 2.9 33.2 + - + -
110A ALA 4.0 9.5 + - - -
112A GLY* 3.3 33.4 - - - -
113A PHE 3.6 16.8 - - - +
114A PHE* 4.0 9.6 - - + +
125A PHE* 3.5 14.4 - - - -
153A PHE* 4.1 9.9 - - - -
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Residues in contact with LEU 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A GLU* 2.8 22.5 + - + +
88A GLU* 3.5 20.9 - - - +
89A LEU 3.3 0.2 - - - -
90A ARG* 1.3 73.2 - - - +
92A ALA* 1.3 62.0 + - - +
94A PHE* 3.1 21.4 + - + +
95A TYR* 4.2 0.5 + - - -
105A PRO* 3.8 22.9 - - + +
106A GLU* 3.8 25.8 - - + +
109A ALA* 3.7 22.6 - - + +
89C LEU* 5.6 0.2 - - - +
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Residues in contact with ALA 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A GLU 3.2 5.5 + - - +
89A LEU 3.2 11.3 + - - +
91A LEU* 1.3 78.3 - - - +
93A SER* 1.3 62.5 + - - +
95A TYR* 3.1 15.1 + - - +
81C PHE* 3.8 16.4 - - + -
83C GLY* 3.3 18.8 - - - -
84C MET* 3.9 26.5 - - + -
89C LEU* 4.2 21.1 - - + -
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Residues in contact with SER 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A MET* 3.9 22.9 - - - -
89A LEU 3.4 2.0 + - - -
90A ARG 2.6 21.6 + - - -
92A ALA* 1.3 77.6 - - - +
94A PHE* 1.3 54.2 + - - +
95A TYR* 3.2 8.2 + - - -
96A ASP* 3.3 9.0 - - - +
114A PHE* 3.5 4.0 - - - +
115A HIS* 2.9 54.9 + - - +
81C PHE* 4.0 8.2 - - - -
83C GLY* 4.8 0.7 - - - +
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Residues in contact with PHE 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A ARG 3.1 29.4 - - - -
91A LEU* 3.1 14.0 + - - +
92A ALA 3.1 1.6 - - - -
93A SER* 1.3 76.9 - - - +
95A TYR* 1.3 61.2 + - - +
96A ASP 3.1 3.1 - - - -
97A TRP* 3.2 56.3 + + + +
105A PRO* 3.5 30.5 - - + +
108A LEU* 3.8 22.7 - - + -
109A ALA* 4.1 9.9 - - + -
113A PHE 3.4 22.9 - - - -
114A PHE* 3.8 7.2 - - - -
115A HIS* 3.6 19.3 - - + -
122A VAL* 3.8 12.8 - - + -
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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