Contacts of the helix formed by residues 95 - 103 (chain C) in PDB entry 3FIW
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 ASP 95 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C LEU* 4.3 0.2 - - + -
21C GLY* 3.3 9.5 - - - -
22C LEU* 2.8 40.9 + - + +
93C ARG 3.3 0.8 + - - -
94C ARG* 1.3 82.8 + - - +
96C GLY* 1.3 59.5 + - - +
97C ALA 3.2 3.1 - - - -
98C ARG* 3.3 31.4 + - + +
99C LEU* 2.9 26.6 + - - +
148C GLN* 3.6 29.4 + - - +
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Residues in contact with GLY 96 (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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59C ALA* 6.0 1.8 - - - +
60C MSE 5.7 0.3 - - - +
90C LEU* 3.5 23.1 - - - +
93C ARG* 3.1 16.0 + - - -
94C ARG 3.0 6.3 + - - -
95C ASP* 1.3 77.9 - - - +
97C ALA* 1.3 56.7 + - - +
99C LEU* 3.7 11.8 - - - +
100C HIS* 2.9 29.5 + - - +
148C GLN* 3.2 2.6 - - - +
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Residues in contact with ALA 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C LEU* 4.1 14.8 + - + -
96C GLY* 1.3 74.3 - - - +
98C ARG* 1.3 59.2 + - - +
100C HIS* 3.3 2.5 + - - +
101C ALA* 2.9 31.2 + - - +
141C VAL* 4.2 8.3 - - + +
144C VAL* 3.7 12.3 - - + -
145C LEU* 3.5 37.5 - - + +
148C GLN* 3.0 19.1 - - - +
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Residues in contact with ARG 98 (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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22C LEU* 3.8 29.6 - - + +
23C ASP* 2.6 41.4 + - - -
95C ASP* 3.3 37.8 + - + +
97C ALA* 1.3 73.4 - - - +
99C LEU* 1.3 61.3 + - - +
101C ALA* 3.8 3.4 - - - +
102C GLY* 2.8 29.8 + - - -
145C LEU* 3.9 17.9 - - + -
148C GLN* 4.5 0.8 - - - +
101D ALA* 6.4 0.9 - - + -
102D GLY* 6.3 3.5 - - - -
104D ARG* 5.8 4.0 - - - +
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Residues in contact with LEU 99 (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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14C LEU* 4.1 3.6 - - + -
17C LEU* 3.7 22.4 - - + -
22C LEU* 4.0 15.1 - - + +
52C LEU* 3.9 36.1 - - + +
55C MSE 3.9 29.6 - - + +
56C ALA* 3.6 27.4 - - + +
59C ALA* 4.0 14.6 - - + -
93C ARG* 5.4 0.7 - - + -
95C ASP 2.9 17.1 + - - +
96C GLY* 3.7 9.4 - - - +
97C ALA 3.4 0.2 - - - -
98C ARG* 1.3 78.0 - - - +
100C HIS* 1.3 60.2 + - - +
102C GLY* 3.5 1.1 + - - -
103C SER* 3.4 16.9 + - - +
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Residues in contact with HIS 100 (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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56C ALA* 4.3 8.9 + - - +
60C MSE 3.7 33.5 - - + +
86C PHE* 3.9 19.8 - + - -
90C LEU* 3.7 11.7 - - + -
96C GLY 2.9 18.8 + - - +
97C ALA* 3.6 4.5 - - - +
99C LEU* 1.3 77.0 - - - +
101C ALA* 1.3 64.8 + - - +
103C SER 3.6 0.5 - - - -
104C ARG* 3.4 35.1 + - + +
105C PRO* 3.5 29.0 - - + +
141C VAL* 4.3 22.1 - - + +
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Residues in contact with ALA 101 (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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97C ALA 2.9 18.5 + - - +
98C ARG* 4.0 4.9 - - - +
100C HIS* 1.3 78.6 - - - +
102C GLY* 1.3 62.8 + - - +
103C SER 3.5 0.7 + - - -
104C ARG* 2.9 41.7 + - - +
141C VAL* 4.5 16.4 - - + -
145C LEU* 4.8 3.1 - - + -
145D LEU* 4.7 14.4 - - + -
149D ALA* 5.3 1.4 - - - +
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Residues in contact with GLY 102 (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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52C LEU* 6.1 0.6 - - - +
98C ARG 2.8 17.5 + - - -
99C LEU 4.0 1.3 - - - -
101C ALA* 1.3 78.4 - - - +
103C SER* 1.3 65.2 + - - +
104C ARG 3.9 0.2 - - - -
98D ARG* 6.3 2.9 - - - -
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Residues in contact with SER 103 (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 ARG 4.8 0.5 + - - -
52C LEU* 3.6 29.2 - - - +
53C THR* 3.8 34.3 + - - +
56C ALA* 3.6 8.3 - - - +
99C LEU 3.4 12.8 + - - -
100C HIS 3.6 3.6 - - - -
101C ALA 3.3 0.2 - - - -
102C GLY* 1.3 81.5 + - - +
104C ARG* 1.3 66.9 + - - +
105C PRO* 3.0 8.5 - - - +
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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