Contacts of the strand formed by residues 93 - 98 (chain A) in PDB entry 2IKS
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 GLN 93 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62A ARG 2.9 7.8 + - - +
63A SER* 3.1 7.3 - - - -
64A ILE 3.0 22.4 + - - +
88A ARG* 2.7 27.1 + - - +
92A TYR* 1.3 72.8 - - - +
94A LEU* 1.3 85.7 + - - +
95A LEU* 3.7 7.1 + - + -
95B LEU* 3.8 28.8 - - + +
96B ILE 3.0 33.5 + - - +
112B HIS* 5.9 0.3 - - - +
113B LEU* 3.7 13.9 - - - +
116B ARG* 3.4 31.0 + - - +
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Residues in contact with LEU 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A ILE* 3.2 32.8 - - + +
66A LEU* 4.1 26.2 - - + -
80A ALA 4.3 1.3 - - - +
83A LEU* 4.1 13.2 - - + -
84A GLU* 3.7 43.0 - - + +
87A ALA* 4.5 14.3 - - + +
88A ARG* 5.3 0.4 - - - +
92A TYR 3.9 2.8 + - - -
93A GLN* 1.3 96.6 + - - +
95A LEU* 1.3 60.9 + - - +
96A ILE* 3.9 25.3 + - + +
122A ILE* 4.6 8.7 - - + -
301A LEU* 5.4 0.9 - - + -
94B LEU 4.8 0.2 - - - +
95B LEU* 4.7 1.2 - - - -
96B ILE* 4.5 6.3 + - - +
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Residues in contact with LEU 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A SER* 3.7 28.9 - - - +
64A ILE 2.8 11.4 + - - +
65A GLY* 3.4 2.9 - - - -
66A LEU 2.8 25.7 + - - -
93A GLN* 3.7 16.8 - - + +
94A LEU* 1.3 73.0 - - - +
96A ILE* 1.3 64.0 + - - +
97A ALA 3.7 0.5 + - - -
113A LEU* 3.7 18.1 - - + +
116A ARG* 3.9 22.7 - - + +
118A VAL* 3.7 18.6 - - + -
93B GLN* 3.8 30.7 - - + +
94B LEU 4.7 1.6 - - - -
95B LEU* 4.8 8.5 - - + -
116B ARG* 5.9 0.2 - - - +
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Residues in contact with ILE 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A LEU* 3.4 14.6 - - + +
68A ILE* 4.3 16.6 - - + -
71A LEU* 4.4 11.0 - - + -
80A ALA* 4.4 18.4 - - + -
84A GLU* 5.6 1.6 - - + -
94A LEU* 3.9 32.4 + - + +
95A LEU* 1.3 73.1 - - - +
97A ALA* 1.3 62.0 + - - +
98A CYS* 4.1 21.1 - - - -
71B LEU* 4.5 9.4 - - + -
84B GLU* 3.9 16.2 - - + +
93B GLN* 3.0 21.9 + - - +
94B LEU* 4.5 3.7 + - - +
96B ILE* 4.1 29.2 - - + -
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Residues in contact with ALA 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A LEU 2.9 7.9 + - - +
67A VAL* 3.2 24.9 - - + +
68A ILE 3.4 3.3 + - - -
95A LEU 3.7 0.2 + - - -
96A ILE* 1.3 75.7 - - - +
98A CYS* 1.3 64.4 + - - +
99A SER 3.8 0.5 + - - -
109A CYS* 3.9 26.9 - - + -
112A HIS* 6.5 0.4 - - + -
113A LEU* 4.3 24.7 - - + -
84B GLU* 3.5 5.6 - - - +
88B ARG* 5.2 3.1 - - - -
93B GLN* 4.9 4.0 - - - +
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Residues in contact with CYS 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A ILE* 3.1 6.1 - - - -
69A PRO 3.5 12.1 - - - +
70A ASP* 3.9 25.4 - - - -
71A LEU* 4.2 10.1 - - - -
96A ILE* 4.1 16.4 - - - -
97A ALA* 1.3 75.8 - - - +
99A SER* 1.3 61.6 + - - +
100A GLU* 3.4 2.0 - - + +
105A ASN* 5.2 0.3 - - - +
109A CYS* 3.6 7.1 - - - -
81B ASN* 5.1 2.5 - - - +
84B GLU* 2.9 35.5 + - - +
88B ARG* 3.2 29.4 + - - +
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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