Contacts of the helix formed by residues 90 - 102 (chain H) in PDB entry 3VON
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 ASN 90 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88H ASP* 3.2 27.1 + - - +
89H GLY* 1.3 76.2 - - - +
91H CYS* 1.3 52.1 + - - +
92H PHE 3.5 2.2 - - - -
93H TYR* 3.1 9.4 + - - +
94H ARG* 2.8 53.1 + - + +
169H ASP* 5.1 1.4 + - - -
172H VAL* 3.8 16.2 - - + +
176H ARG* 2.9 31.3 + - - +
211H MET* 4.1 14.9 - - - +
212H CYS* 3.4 23.9 + - - +
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Residues in contact with CYS 91 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85H THR* 4.0 17.3 + - - +
86H ARG 3.2 25.8 - - - -
87H PRO* 4.3 8.5 - - - -
88H ASP* 4.4 0.6 + - - -
89H GLY* 3.3 12.5 + - - -
90H ASN* 1.3 76.4 - - - +
92H PHE* 1.3 55.1 + - - +
94H ARG* 3.0 6.8 + - - +
95H ALA* 2.8 38.7 + - + +
214H GLU* 6.0 1.8 - - - -
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Residues in contact with PHE 92 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90H ASN 3.5 0.6 - - - -
91H CYS* 1.3 78.1 - - - +
93H TYR* 1.3 72.8 + + + +
95H ALA* 4.7 4.5 - - + -
96H PHE* 3.2 43.3 + + + +
215H SER* 3.6 37.2 - - - +
219H HIS 4.2 1.8 - - - -
220H ILE* 3.5 60.3 - - + -
223H LEU* 4.2 24.5 - - + -
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Residues in contact with TYR 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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89H GLY 5.2 0.4 - - - -
90H ASN* 3.1 10.4 + - - +
92H PHE* 1.3 92.5 - + + +
94H ARG* 1.3 63.8 + - - +
96H PHE* 5.0 1.6 - + - -
97H GLY* 3.5 7.8 + - - -
171H LEU* 4.1 6.2 - - - +
172H VAL* 3.8 21.9 - - + +
175H LEU* 3.5 50.8 - - + +
176H ARG* 3.8 47.3 - - + +
179H THR* 3.4 31.4 + - - +
208H VAL* 4.4 3.6 + - - +
213H LYS 5.2 0.2 - - - -
215H SER* 3.7 20.2 - - - -
219H HIS* 3.1 28.5 + - - +
223H LEU* 5.0 3.1 - - + -
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Residues in contact with ARG 94 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47H LEU* 3.5 39.5 - - - +
48H VAL* 4.4 10.3 - - + +
85H THR* 3.8 18.6 - - + -
86H ARG* 5.3 3.2 - - - +
88H ASP* 4.7 12.3 + - - +
90H ASN* 2.8 38.3 + - + +
91H CYS* 3.3 9.0 - - - +
93H TYR* 1.3 78.9 - - - +
95H ALA* 1.3 61.6 - - - +
97H GLY 3.7 0.2 + - - -
98H PHE* 3.3 22.9 + - - +
162H PHE* 3.9 13.1 - - - -
165H GLN* 4.6 1.8 - - - +
168H SER* 3.0 40.3 + - - -
169H ASP* 2.6 28.5 + - - +
171H LEU* 5.6 1.4 - - - +
172H VAL* 3.3 15.7 - - - +
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Residues in contact with ALA 95 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85H THR* 4.6 13.9 - - + +
91H CYS 2.8 20.3 + - - +
92H PHE* 4.4 4.7 - - + +
94H ARG* 1.3 71.7 - - - +
96H PHE* 1.3 55.8 + - - +
98H PHE* 3.2 3.9 + - - +
99H SER* 2.7 40.8 + - - -
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Residues in contact with PHE 96 (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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92H PHE* 3.2 34.1 + + + +
93H TYR* 4.9 1.8 - + - +
95H ALA* 1.3 78.4 - - - +
97H GLY* 1.3 66.9 + - - +
99H SER* 4.5 4.9 - - - +
100H HIS* 3.2 47.1 + + + +
114H PHE* 5.0 17.9 - + - -
142H PHE* 6.1 0.4 - + - -
175H LEU* 3.8 31.6 - - + -
223H LEU* 4.2 26.9 - - + -
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Residues in contact with GLY 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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93H TYR 3.5 18.4 + - - -
95H ALA 3.3 0.6 - - - -
96H PHE* 1.3 82.8 - - - +
98H PHE* 1.3 56.0 + - - +
100H HIS* 5.1 0.2 - - - +
101H LEU* 3.3 25.8 + - - +
142H PHE* 6.5 0.4 - - - -
162H PHE* 3.3 23.2 - - - -
171H LEU* 4.2 9.2 - - - -
175H LEU* 4.3 6.1 - - - -
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Residues in contact with PHE 98 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48H VAL* 4.3 12.3 - - + -
83H ARG* 3.3 47.1 - - - -
94H ARG 3.3 14.2 + - - +
95H ALA* 3.2 4.6 + - - +
96H PHE 3.2 0.4 - - - -
97H GLY* 1.3 75.5 - - - +
99H SER* 1.3 61.1 + - - +
100H HIS 3.2 2.2 - - - -
101H LEU* 4.3 1.1 - - - +
102H GLU* 2.9 58.3 + - + +
155H VAL* 4.1 17.9 - - + -
158H LEU* 3.6 36.7 - - + +
159H LEU* 3.8 8.5 - - + -
162H PHE* 3.5 31.2 - + + -
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Residues in contact with SER 99 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95H ALA* 2.7 25.1 + - - -
96H PHE* 4.4 3.8 - - - -
98H PHE* 1.3 74.8 - - - +
100H HIS* 1.3 58.0 + - - +
102H GLU* 4.2 11.7 + - - +
103H ALA* 3.3 21.8 + - - +
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Residues in contact with HIS 100 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96H PHE* 3.2 36.8 + + + +
97H GLY 5.1 0.2 - - - +
99H SER* 1.3 77.2 - - - +
101H LEU* 1.3 61.3 + - + +
102H GLU 3.3 1.3 - - - -
103H ALA* 3.7 9.7 - - + +
104H LEU* 3.0 53.1 + - + +
110H GLU* 4.2 18.2 + - - -
114H PHE* 3.8 35.1 - + + -
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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
----------------------------------------------------------
97H GLY* 3.3 22.5 + - - +
98H PHE 3.5 1.0 + - - -
100H HIS* 1.3 76.0 - - + +
102H GLU* 1.3 61.3 + - - +
104H LEU* 3.8 16.7 + - + +
105H LEU* 3.5 25.1 + - - +
114H PHE* 4.6 7.9 - - + -
142H PHE* 6.2 2.2 - - + -
145H LEU* 3.4 37.7 - - + +
146H ILE* 4.2 18.8 - - + -
149H VAL* 3.7 18.6 - - + +
158H LEU* 3.8 14.9 - - + +
162H PHE* 3.8 21.3 - - + -
171H LEU* 5.0 5.8 - - + -
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Residues in contact with GLU 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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51H ARG* 4.4 12.9 + - - -
83H ARG* 3.9 14.7 + - - -
98H PHE* 2.9 40.2 + - + +
99H SER* 4.2 8.7 - - - +
101H LEU* 1.3 78.7 - - - +
103H ALA* 1.3 57.5 + - - +
105H LEU* 3.2 24.5 - - + +
106H ASP* 4.7 2.4 - - - +
155H VAL* 3.4 33.6 - - + +
158H LEU* 3.7 11.2 - - + +
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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