Contacts of the strand formed by residues 120 - 127 (chain A) in PDB entry 1OIK
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 120 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A LEU* 4.6 14.8 - - + -
118A PRO* 3.3 3.1 + - - +
119A LYS* 1.3 93.3 - - + +
121A SER* 1.3 62.8 + - - +
256A ILE* 4.8 4.5 - - + -
257A TRP 3.1 17.3 - - - +
259A ASN* 3.9 6.7 - - - +
281A THR* 3.5 6.9 + - - -
282A LEU* 3.0 39.7 + - + +
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Residues in contact with SER 121 (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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110A ASP* 3.8 5.6 + - - -
118A PRO* 5.3 0.5 - - - +
120A ALA* 1.3 73.7 - - - +
122A ILE* 1.3 64.1 + - - +
123A LEU 4.2 0.2 - - - -
255A ALA 3.7 0.7 - - - +
256A ILE* 3.2 25.5 - - - +
257A TRP* 3.2 46.0 + - - +
259A ASN* 5.8 0.2 - - - -
279A ARG* 3.1 21.0 + - - -
280A VAL 3.4 4.7 - - - -
281A THR* 2.9 22.0 + - - -
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Residues in contact with ILE 122 (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 LEU* 6.3 0.4 - - + -
68A GLN* 3.3 19.9 + - + +
71A PHE* 4.2 17.5 - - + -
72A ALA* 3.5 38.1 - - + -
75A LEU* 4.2 7.6 - - + -
121A SER* 1.3 78.3 - - - +
123A LEU* 1.3 61.1 + - - +
254A VAL* 3.9 21.5 - - + -
255A ALA 3.4 3.6 - - - -
256A ILE* 3.9 20.6 - - + -
279A ARG* 3.2 4.3 - - - -
280A VAL* 2.8 37.4 + - + +
282A LEU* 4.0 22.9 - - + -
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Residues in contact with LEU 123 (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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122A ILE* 1.3 76.4 - - - +
124A ARG* 1.3 59.1 + - - +
137A TRP* 5.2 0.9 - - + -
249A TRP* 3.8 26.3 - - + -
254A VAL* 3.2 6.3 - - - -
255A ALA 2.8 38.3 + - - +
257A TRP* 3.6 28.0 - - + -
277A VAL* 3.7 29.8 - - + -
278A ARG 3.5 8.3 - - - +
279A ARG* 3.3 26.7 - - + -
1301A AKG 3.8 40.6 - - + +
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Residues in contact with ARG 124 (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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60A GLN 4.4 5.2 - - - -
63A LEU* 3.6 45.8 + - - +
64A ASP* 3.6 19.7 - - - +
65A ASP* 3.2 25.7 + - - -
68A GLN* 3.0 32.4 + - - +
123A LEU* 1.3 73.9 - - - +
125A SER* 1.3 69.7 + - - +
126A VAL* 3.5 28.7 + - - +
249A TRP* 4.8 1.1 - - - -
252A GLY* 4.9 4.5 - - - -
253A ASP 3.5 10.3 - - - +
254A VAL* 3.9 10.8 - - + +
277A VAL* 3.3 7.2 - - - +
278A ARG* 2.8 39.0 + - - +
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Residues in contact with SER 125 (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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124A ARG* 1.3 75.4 + - - +
126A VAL* 1.3 57.0 + - - +
127A VAL 4.2 2.1 + - - -
128A ALA* 3.6 24.6 + - - +
249A TRP* 3.6 26.3 - - - +
250A GLU 3.5 22.1 + - - -
251A ALA* 3.5 2.6 - - - -
252A GLY* 2.7 31.7 + - - -
253A ASP 2.9 10.3 + - - -
276A ILE 4.2 3.6 - - - -
277A VAL* 4.2 7.5 - - - +
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Residues in contact with VAL 126 (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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124A ARG* 3.9 35.4 - - - +
125A SER* 1.3 71.2 - - - +
127A VAL* 1.3 69.1 + - + +
128A ALA 4.3 0.2 - - - -
251A ALA* 3.6 18.9 - - - +
276A ILE* 3.0 25.4 + - + +
278A ARG* 4.2 40.6 - - + +
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Residues in contact with VAL 127 (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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125A SER* 4.2 3.3 + - - -
126A VAL* 1.3 85.7 - - + +
128A ALA* 1.3 66.5 + - - +
251A ALA* 5.2 0.4 - - - -
274A PRO* 3.8 29.2 - - + +
275A ARG* 3.3 8.3 - - - +
276A ILE* 2.8 65.0 + - + +
277A VAL* 5.0 1.2 - - - +
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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