Contacts of the strand formed by residues 108 - 113 (chain X) in PDB entry 1IRA
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 THR 108 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18X VAL* 3.7 27.8 - - + -
104X ASP* 3.5 7.2 - - - +
105X SER* 2.8 39.9 + - - -
106X GLY 4.2 0.5 - - - +
107X PRO* 1.3 90.8 - - + +
109X THR* 1.3 64.2 + - - +
145X LYS* 3.4 31.2 - - + +
146X PHE 3.2 11.2 - - - +
147X TYR* 4.1 14.4 - - + +
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Residues in contact with THR 109 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102X ARG* 3.4 35.2 + - + +
103X SER 3.3 13.0 - - - +
104X ASP* 3.2 12.0 + - - +
105X SER* 5.5 1.1 - - - -
107X PRO 5.0 1.0 + - - -
108X THR* 1.3 74.5 - - - +
110X SER* 1.3 73.0 - - - +
111X PHE* 3.9 19.5 - - + -
144X THR 3.6 0.3 - - - +
145X LYS* 3.5 8.1 - - - +
146X PHE* 2.8 32.8 + - - -
148X PHE* 3.6 25.6 + - + +
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Residues in contact with SER 110 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101X ILE 3.5 1.4 - - - +
102X ARG* 3.6 2.9 - - - -
103X SER* 2.8 44.9 + - - -
105X SER* 6.5 0.9 - - - -
109X THR* 1.3 78.0 - - - +
111X PHE* 1.3 67.1 + - - +
112X GLU 4.2 0.2 - - - -
120X PHE* 3.8 21.0 - - - +
144X THR* 3.4 24.8 + - - -
145X LYS* 5.3 4.5 - - - -
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Residues in contact with PHE 111 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15X ILE* 4.2 19.5 - - + -
56X LEU* 4.2 20.4 - - + -
58X LEU* 4.1 17.5 - - + -
100X PHE* 4.2 18.4 - - + -
101X ILE 3.5 2.5 - - - -
102X ARG* 4.4 9.9 - - + -
109X THR* 3.9 22.0 - - + -
110X SER* 1.3 80.5 + - - +
112X GLU* 1.3 60.0 + - - +
113X SER 4.1 0.2 + - - -
120X PHE* 3.2 7.1 - - - +
121X LEU* 2.9 56.4 + - + +
144X THR 4.9 0.8 + - - -
146X PHE* 4.5 11.6 - + + -
148X PHE* 3.4 48.0 - + + -
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Residues in contact with GLU 112 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100X PHE* 3.1 6.7 - - - -
101X ILE* 2.8 63.1 + - + +
103X SER* 6.5 0.4 - - - -
110X SER 4.2 0.4 - - - -
111X PHE* 1.3 73.6 - - - +
113X SER* 1.3 72.7 + - - +
117X PRO* 3.7 7.7 - - - +
118X GLY* 2.9 26.2 + - - +
119X TRP 3.5 10.5 - - - +
120X PHE* 3.8 29.8 - - + -
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Residues in contact with SER 113 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69X CYS* 3.3 21.1 - - - +
97X ARG 5.1 1.4 + - - -
99X ALA 4.1 1.1 + - - -
100X PHE* 3.8 19.5 - - - -
101X ILE* 5.0 1.0 - - - +
111X PHE 4.1 0.2 + - - -
112X GLU* 1.3 74.3 - - - +
114X ALA* 1.3 64.0 + - - +
115X ALA* 3.5 2.9 + - - +
116X CYS* 2.9 51.5 + - - +
117X PRO* 3.5 6.9 - - - +
119X TRP* 2.8 16.8 + - - -
133X LEU* 4.9 2.7 - - - -
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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