Contacts of the strand formed by residues 93 - 99 (chain C) in PDB entry 3IFP
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 ALA 93 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40C ARG* 4.2 12.1 - - - -
41C GLN 3.6 28.3 - - - +
42C PRO* 3.7 7.4 - - + -
43C SER 5.1 1.1 - - - +
90C ALA 5.5 0.4 - - - +
91C ASP 3.2 4.5 + - - +
92C THR* 1.3 80.0 - - - +
94C THR* 1.3 59.5 + - - +
95C TYR* 3.5 19.4 - - + -
118C THR* 3.8 1.1 - - - -
119C LEU 2.8 36.3 + - - -
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Residues in contact with THR 94 (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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40C ARG* 3.1 2.4 - - - -
41C GLN* 2.6 45.4 + - - +
93C ALA* 1.3 73.4 - - - +
95C TYR* 1.3 63.1 + - - +
96C TYR* 3.7 33.2 + - + +
115C GLN 5.2 0.4 - - - +
116C GLY* 3.9 15.9 - - - +
117C THR 3.2 11.2 - - - +
118C THR* 3.3 18.2 + - - +
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Residues in contact with TYR 95 (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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6C GLU* 3.7 8.8 - - - +
18C LEU* 4.4 1.6 - - + -
20C LEU* 3.6 30.3 - - + -
38C TRP* 4.4 7.6 - + + -
39C ILE 3.7 2.7 - - - -
40C ARG* 3.0 44.9 + - + -
50C LEU* 3.7 16.8 - - + -
82C LEU* 4.6 3.1 - - + -
84C ILE* 3.8 18.5 - - + +
91C ASP* 2.6 33.4 + - - +
93C ALA* 3.5 24.2 - - + -
94C THR* 1.3 73.9 - - - +
96C TYR* 1.3 61.3 + - - +
116C GLY* 3.5 1.6 - - - -
117C THR* 2.8 39.9 + - + +
119C LEU* 3.8 20.1 - - + +
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Residues in contact with TYR 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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6C GLU* 3.4 4.0 - - - +
38C TRP* 3.3 11.7 - - - -
39C ILE* 2.5 45.6 + - + +
41C GLN* 4.0 17.1 + - + -
47C LEU* 4.4 10.8 - - + -
94C THR* 3.7 24.9 - - + +
95C TYR* 1.3 74.4 - - - +
97C CYS* 1.3 60.5 + - - +
113C TRP* 3.9 29.2 - + + -
114C GLY 3.6 13.0 - - - +
115C GLN 3.6 9.7 + - - -
116C GLY* 3.3 29.8 - - - -
43D GLN* 3.3 21.0 + - - -
47D GLN 3.7 5.9 + - - -
48D SER* 3.8 17.5 - - - -
49D PRO* 4.4 7.0 - - + -
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Residues in contact with CYS 97 (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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4C LEU* 3.7 13.5 - - - +
5C LYS 4.9 0.2 - - - -
6C GLU* 2.8 23.7 + - - -
22C CYS* 2.0 52.3 - - + -
36C VAL* 3.9 7.6 - - + -
37C SER 3.2 12.8 - - - +
38C TRP* 4.1 11.4 - - + -
96C TYR* 1.3 75.7 - - - +
98C ALA* 1.3 59.0 + - - +
113C TRP* 3.5 1.6 - - - +
114C GLY 3.0 24.4 + - - -
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Residues in contact with ALA 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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4C LEU* 4.4 1.8 - - - -
36C VAL* 3.2 8.1 - - - +
37C SER* 3.1 29.8 + - - -
38C TRP* 5.1 0.2 - - - +
39C ILE* 4.4 6.8 - - + +
96C TYR 4.2 0.4 - - - -
97C CYS* 1.3 73.7 - - - +
99C ARG* 1.3 60.7 + - - +
110C PHE* 3.4 30.9 - - + -
112C TYR 3.1 11.4 - - - +
113C TRP* 3.9 26.0 - - + -
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Residues in contact with ARG 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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2C VAL* 4.8 5.7 - - - +
4C LEU* 4.3 2.3 - - + +
26C GLY 5.5 0.2 + - - -
27C PHE* 3.8 44.3 - - + +
34C MET* 3.6 26.7 - - - +
35C GLY 3.6 12.6 - - - +
36C VAL* 4.5 2.0 - - - +
98C ALA* 1.3 72.8 - - - +
100C ARG* 1.3 67.2 + - - +
101C ARG* 2.8 34.0 - - - +
109C TYR 3.3 1.6 - - - +
110C PHE* 3.2 26.3 - - - -
111C ASP* 2.4 45.4 + - - +
112C TYR* 2.8 38.5 + - + +
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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