Contacts of the helix formed by residues 107 - 113 (chain C) in PDB entry 1F3F
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 107 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105B PRO* 4.0 6.6 - - - +
31C ARG* 3.6 1.3 - - - -
93C LEU 4.1 6.5 - - - -
94C MET 3.3 13.2 - - - -
95C ILE 3.6 8.1 - - - -
96C GLY* 3.7 11.4 - - - -
103C SER* 3.5 8.8 - - - -
104C ALA* 2.6 26.3 + - - +
105C PRO 3.3 0.4 + - - -
106C GLY* 1.3 78.1 - - - +
108C ILE* 1.3 59.4 + - - +
110C GLY* 2.9 15.2 + - - -
111C ASP* 2.8 30.7 + - - -
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Residues in contact with ILE 108 (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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28C ILE* 4.1 20.4 - - + -
31C ARG* 3.5 33.7 - - + +
32C TYR* 3.7 37.7 - - + +
94C MET* 2.8 21.0 + - + +
95C ILE* 4.1 5.6 - - - +
107C SER* 1.3 71.4 - - - +
109C ARG* 1.3 60.3 + - - +
111C ASP 3.3 0.3 + - - -
112C PHE* 2.9 48.7 + - + +
120C ILE* 4.2 10.5 - - + -
121C ILE* 4.0 27.4 - - + -
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Residues in contact with ARG 109 (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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35A LYS* 3.4 5.9 + - - -
92C ARG* 3.8 4.0 - - - +
95C ILE* 2.9 43.1 + - + +
97C VAL 3.0 31.3 + - - -
98C THR* 3.3 3.5 - - - +
100C PRO* 3.7 9.8 - - + +
103C SER* 3.6 12.1 - - - +
108C ILE* 1.3 73.2 - - - +
110C GLY* 1.3 64.1 + - - +
113C GLY 3.0 22.9 + - - +
119C ASN* 3.1 53.6 + - + +
120C ILE* 4.1 8.1 - - + -
121C ILE* 2.8 24.9 + - + -
122C GLY* 4.1 0.2 - - - -
164C D4T 2.8 43.9 + - - -
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Residues in contact with GLY 110 (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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35A LYS* 2.6 27.0 + - - +
94A MET* 4.9 7.4 - - - +
103C SER* 3.2 30.2 - - - +
104C ALA 3.5 4.0 - - - -
105C PRO* 4.6 4.6 - - - +
107C SER* 2.9 18.0 + - - -
109C ARG* 1.3 78.1 - - - +
111C ASP* 1.3 60.6 + - - +
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Residues in contact with ASP 111 (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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31A ARG 4.4 2.1 - - - +
34A LYS* 3.6 3.9 - - + +
35A LYS* 3.3 24.0 + - - +
94A MET* 5.4 2.8 - - - +
106A GLY 5.1 1.2 - - - +
31C ARG* 2.7 34.7 + - - +
105C PRO* 3.6 8.0 - - - +
106C GLY* 2.8 29.6 + - - -
107C SER 2.8 18.2 + - - +
108C ILE 4.0 1.8 - - - +
110C GLY* 1.3 80.7 - - - +
112C PHE* 1.3 70.3 + - + +
113C GLY 4.0 0.2 - - - -
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Residues in contact with PHE 112 (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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34A LYS* 3.5 44.6 - - + +
35A LYS 3.2 10.6 - - - +
153A LEU* 3.8 0.2 - - - +
22C ARG* 2.7 34.4 + - - -
24C LEU* 4.0 33.4 - - + -
27C GLU* 3.6 37.5 - - + -
28C ILE* 5.5 1.8 - - + -
31C ARG* 3.4 28.3 - - - -
108C ILE* 2.9 34.8 + - + +
111C ASP* 1.3 87.7 - - + +
113C GLY* 1.3 55.0 + - - +
120C ILE* 3.8 10.5 - - + -
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Residues in contact with GLY 113 (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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35A LYS* 2.9 29.0 + - - -
153A LEU* 4.5 2.2 - - - -
22C ARG* 4.5 2.5 - - - -
100C PRO* 3.2 15.8 - - - +
109C ARG 3.0 10.6 + - - -
111C ASP 4.0 0.4 - - - -
112C PHE* 1.3 79.6 - - - +
114C VAL* 1.3 64.6 + - - -
118C ARG 4.7 2.9 - - - -
120C ILE* 3.6 15.1 - - - +
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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