Contacts of the strand formed by residues 133 - 139 (chain A) in PDB entry 1O7F
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 SER 133 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62A GLU 4.1 0.2 - - - +
63A ASN* 3.4 6.2 - - - +
64A LEU* 2.6 44.3 + - - +
85A ALA 3.2 13.5 - - - -
87A SER 3.1 27.4 + - - -
88A LEU* 5.0 6.5 - - - -
129A THR* 4.2 14.3 - - - +
131A GLU 2.7 20.4 + - - -
132A SER* 1.3 72.4 + - - +
134A GLU* 1.3 65.5 + - - +
135A LEU* 5.0 6.5 - - - -
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Residues in contact with GLU 134 (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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15A TRP* 4.1 11.6 - - - -
16A ILE* 4.2 4.5 - - - +
37A ARG* 5.3 4.6 + - - -
61A TYR* 2.4 39.0 + - + +
62A GLU 3.4 4.7 - - - -
63A ASN* 3.8 13.0 - - - +
84A LEU* 2.8 32.7 + - + -
85A ALA* 2.9 35.5 + - + +
132A SER* 6.1 0.2 - - - +
133A SER* 1.3 77.7 - - - +
135A LEU* 1.3 64.7 + - - +
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Residues in contact with LEU 135 (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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61A TYR* 3.7 8.8 - - - -
62A GLU* 2.8 40.4 + - + +
64A LEU* 4.1 18.4 - - + -
70A LEU* 3.9 33.9 - - + -
81A TYR* 3.9 17.5 - - + -
82A ALA 3.4 5.6 - - - +
83A VAL* 3.8 32.5 - - + +
84A LEU* 4.1 5.6 - - - +
88A LEU* 4.2 18.2 - - + -
113A PHE* 4.6 6.1 - - + -
129A THR* 5.5 0.9 - - + -
133A SER* 5.0 6.1 - - - +
134A GLU* 1.3 83.9 - - - +
136A LEU* 1.3 60.7 + - - +
137A ARG 4.0 0.6 + - - +
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Residues in contact with LEU 136 (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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19A LEU* 3.7 26.7 - - + -
38A LEU* 3.8 25.4 - - + -
44A PHE* 3.5 37.9 - - + -
55A ILE* 4.2 13.2 - - + +
59A GLY* 4.6 4.7 - - - -
60A TYR 3.3 22.7 - - - +
80A TRP* 5.4 3.0 - - + -
81A TYR* 3.2 5.5 - - - +
82A ALA* 2.9 39.2 + - + +
84A LEU* 3.9 12.8 - - + +
135A LEU* 1.3 72.8 - - - +
137A ARG* 1.3 63.1 + - - +
138A ILE* 5.3 2.7 - - + -
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Residues in contact with ARG 137 (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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59A GLY* 3.4 4.0 - - - -
60A TYR* 2.8 65.2 + - + +
62A GLU* 2.8 40.8 + - + -
79A ASN* 3.1 31.1 + - - +
80A TRP 3.2 4.3 - - - +
81A TYR* 3.6 27.4 - - + -
135A LEU 4.0 1.0 + - - -
136A LEU* 1.3 75.0 - - - +
138A ILE* 1.3 64.5 + - - +
139A GLU* 2.8 33.3 + - - +
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Residues in contact with ILE 138 (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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55A ILE* 3.5 41.5 - - + -
58A CYS* 4.2 7.6 - - - -
59A GLY* 4.2 13.5 - - - -
79A ASN* 3.4 4.5 - - - -
80A TRP* 2.9 61.7 + - + +
136A LEU* 5.3 3.6 - - + -
137A ARG* 1.3 78.5 - - - +
139A GLU* 1.3 76.2 + - - +
142A ASP* 3.9 11.4 - - + +
143A PHE* 3.7 24.4 - - + +
146A LEU* 4.2 8.3 - - + -
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Residues in contact with GLU 139 (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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58A CYS 5.3 0.2 + - - -
60A TYR* 3.6 28.8 + - + -
78A THR 3.7 2.9 - - - +
79A ASN* 3.4 8.6 + - - +
137A ARG* 2.8 33.3 + - - +
138A ILE* 1.3 79.2 - - - +
140A GLN* 1.3 67.0 + - - +
141A GLU* 3.5 3.4 - - + +
142A ASP* 3.3 18.7 + - - +
143A PHE* 2.9 20.7 + - - +
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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