Contacts of the helix formed by residues 99 - 103 (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 ASN 99 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85A LYS* 5.2 5.9 + - - +
97C VAL* 3.2 7.6 - - + +
98C THR* 1.3 78.1 - - - +
100C PRO* 1.3 69.2 - - - +
101C LEU* 2.9 35.8 - - - +
102C ALA* 3.0 25.0 + - + +
103C SER* 3.1 11.8 + - - -
114C VAL 4.3 2.4 + - - -
116C VAL* 3.9 19.2 - - + +
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Residues in contact with PRO 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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35A LYS* 3.0 18.5 + - - -
98C THR 3.1 9.0 - - - +
99C ASN* 1.3 89.7 - - - +
101C LEU* 1.3 59.9 + - - +
102C ALA 3.1 0.2 - - - -
103C SER* 3.2 20.8 + - - +
109C ARG* 3.7 18.0 - - + +
113C GLY* 3.2 32.5 - - - +
114C VAL 3.6 1.1 - - - +
115C ASP 3.6 25.6 - - - +
116C VAL 3.9 0.7 - - - +
119C ASN* 3.6 27.4 - - + -
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Residues in contact with LEU 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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35A LYS* 4.4 2.7 + - - +
37A PHE* 4.1 0.4 - - + -
85A LYS* 3.5 55.6 - - + +
86A GLY* 4.3 7.2 - - - +
90A SER* 3.9 32.6 + - - +
93A LEU* 3.7 17.3 - - - +
99C ASN* 2.9 14.9 - - - +
100C PRO* 1.3 78.4 - - - +
102C ALA* 1.3 58.9 + - - +
113C GLY 4.5 2.0 - - - +
114C VAL* 3.2 41.3 - - + +
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Residues in contact with ALA 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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93A LEU* 4.4 7.0 - - - +
97C VAL* 3.8 15.1 - - + +
99C ASN* 3.0 23.8 + - + +
101C LEU* 1.3 77.5 - - - +
103C SER* 1.3 62.5 + - - +
104C ALA 3.7 1.7 + - - -
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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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35A LYS* 4.7 1.0 + - - -
93A LEU* 3.6 12.2 - - - +
96C GLY* 4.0 0.9 - - - -
97C VAL* 2.9 35.2 + - - +
99C ASN 3.1 12.1 + - - -
100C PRO 3.2 7.7 + - - +
102C ALA* 1.3 79.8 - - - +
104C ALA* 1.3 64.9 + - - +
105C PRO* 3.7 0.7 - - - +
107C SER* 3.5 5.8 - - - -
109C ARG* 3.6 7.2 - - - +
110C GLY* 3.2 34.4 - - - +
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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