Contacts of the strand formed by residues 97 - 103 (chain C) in PDB entry 5ITY
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 97 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C SER* 3.9 5.4 - - - -
93C LEU* 4.1 5.8 - - + -
94C PRO* 3.1 23.8 + - + +
95C ARG 3.2 0.8 + - - -
96C HIS* 1.3 74.1 - - - +
98C HIS* 1.3 59.7 + - - +
99C LEU 3.6 1.8 - - - -
100C ARG* 2.6 52.4 + - - +
113C CYS* 4.0 20.6 - - + -
114C PHE 3.7 6.3 - - - -
115C VAL* 3.9 5.2 - - - -
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Residues in contact with HIS 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C LYS* 3.7 1.4 - - - +
30C SER* 2.8 45.5 + - - +
32C VAL* 4.0 13.4 - - + +
33C SER* 4.5 7.8 - - - -
96C HIS* 2.9 36.4 + - + +
97C ALA* 1.3 73.2 + - - +
99C LEU* 1.3 58.3 + - - +
100C ARG* 5.0 0.4 - - - -
114C PHE* 2.9 15.4 + - + +
116C ASP* 2.8 40.2 + - + -
119C ARG* 3.7 32.0 + - + +
123C TRP* 3.4 22.5 - - + -
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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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27C VAL* 3.6 24.2 - - + -
28C GLU 3.5 10.5 - - - +
29C LYS* 4.0 7.6 - - + +
38C VAL* 3.7 13.5 - - + -
75C LEU* 4.1 2.0 - - + -
77C PHE* 3.7 21.8 - - + -
98C HIS* 1.3 73.8 - - - +
100C ARG* 1.3 65.8 + - - +
101C PHE* 3.7 21.8 - - + -
112C LEU 4.0 0.2 - - - +
113C CYS* 3.2 3.1 - - - -
114C PHE* 2.7 40.0 + - + +
123C TRP* 3.2 55.2 - - + +
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Residues in contact with ARG 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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27C VAL* 3.5 7.8 - - - +
28C GLU* 2.7 62.1 + - - +
29C LYS 4.2 2.2 + - - -
30C SER* 3.8 25.2 - - - +
31C SER 5.1 0.8 - - - +
93C LEU* 3.7 32.6 - - + +
94C PRO 5.3 0.2 + - - -
97C ALA* 2.6 41.0 + - + +
99C LEU* 1.3 83.2 - - - +
101C PHE* 1.3 65.0 + - - +
102C TYR* 3.6 27.7 + - + +
111C ALA* 5.4 0.7 - - + -
112C LEU 3.4 4.5 - - - +
113C CYS* 4.0 12.8 - - - -
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Residues in contact with PHE 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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23C PHE* 3.4 20.6 - - + -
26C CYS 5.0 1.3 - - - -
27C VAL* 3.4 23.8 - - + -
38C VAL* 5.1 0.4 - - + -
45C TYR* 4.1 4.0 - - - +
47C ILE* 4.1 9.2 - - + -
58C LEU* 4.1 17.5 - - + -
60C LEU* 3.7 36.6 - - + -
75C LEU* 4.0 13.7 - - + -
77C PHE* 4.9 1.1 - + - -
85C PHE* 4.8 5.4 - + - -
99C LEU* 3.7 39.3 - - + -
100C ARG* 1.3 75.1 - - - +
102C TYR* 1.3 63.6 + - - +
111C ALA* 3.4 4.7 - - - +
112C LEU* 2.5 62.0 + - + +
114C PHE 5.1 0.9 - - - -
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Residues in contact with TYR 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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23C PHE* 2.7 28.7 - - - -
24C GLY 2.8 25.7 + - - +
25C GLY* 5.8 0.9 - - - -
26C CYS 4.1 10.7 + - - -
28C GLU* 3.0 45.0 + - + -
45C TYR* 3.9 5.1 + - - -
90C ARG* 3.5 41.7 - - + -
93C LEU* 4.2 7.4 - - + +
100C ARG* 3.6 34.2 - - + -
101C PHE* 1.3 76.7 - - - +
103C THR* 1.3 64.5 + - - +
110C LEU 3.9 3.1 - - - -
111C ALA* 4.1 15.0 - - + -
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Residues in contact with THR 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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21C LEU* 4.9 9.0 - - + -
22C VAL 3.5 23.8 - - - +
23C PHE* 4.0 4.0 - - + +
24C GLY* 3.4 12.1 + - - +
102C TYR* 1.3 83.1 - - - +
104C ALA* 1.3 66.8 + - - +
107C GLY* 4.6 2.2 - - - -
108C PRO* 2.9 41.2 + - + +
109C ARG* 4.3 0.9 - - - -
110C LEU* 2.5 39.2 + - + +
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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