Contacts of the strand formed by residues 154 - 161 (chain Y) in PDB entry 1OFU
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 154 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57X HIS* 3.6 18.8 + - - -
43Y PRO 3.1 10.7 + - - -
44Y ALA* 3.0 29.1 - - - +
45Y ALA 3.0 24.3 + - - +
47Y SER* 4.8 3.1 + - - -
121Y LEU* 3.5 5.6 - - - +
127Y HIS 2.9 18.5 + - - +
128Y THR* 3.3 14.3 - - + +
129Y VAL 2.9 26.5 + - - -
153Y ALA* 1.3 73.6 - - - +
155Y SER* 1.3 61.4 + - - +
156Y LEU* 4.0 0.9 - - + -
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Residues in contact with SER 155 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45Y ALA 3.0 13.9 + - - +
46Y PHE* 3.5 22.1 - - - -
47Y SER* 3.0 28.1 + - - +
121Y LEU* 3.8 25.9 - - - +
129Y VAL 3.7 5.3 + - - -
131Y SER* 5.1 2.1 + - - -
144Y LEU* 3.6 19.7 - - - +
148Y ALA* 4.1 7.6 - - - +
153Y ALA 4.1 0.8 + - - -
154Y GLN* 1.3 73.7 - - - +
156Y LEU* 1.3 60.3 + - - +
157Y ASN 4.2 0.2 - - - -
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Residues in contact with LEU 156 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61X LEU* 4.0 34.1 - - + -
47Y SER* 3.6 15.0 - - - +
49Y LEU* 4.2 14.1 - - + +
65Y ILE* 4.8 5.2 - - + -
69Y LEU* 3.9 28.0 - - + -
128Y THR* 4.2 11.4 - - + -
129Y VAL 3.0 11.1 + - - +
130Y VAL* 3.1 14.1 - - + +
131Y SER* 2.8 26.5 + - - +
154Y GLN* 3.9 1.1 + - + -
155Y SER* 1.3 76.7 + - - +
157Y ASN* 1.3 69.1 + - - +
158Y ILE* 4.2 18.8 - - + -
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Residues in contact with ASN 157 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46Y PHE* 3.9 25.7 - - + -
47Y SER 3.1 8.0 + - - +
48Y GLU* 3.1 22.8 + - - +
49Y LEU 2.8 26.5 + - - -
131Y SER* 3.0 20.4 - - - +
133Y LEU* 2.7 49.9 + - - +
136Y LEU* 3.7 12.1 - - - +
144Y LEU* 5.2 0.4 - - + -
155Y SER 4.2 0.2 - - - -
156Y LEU* 1.3 75.5 - - - +
158Y ILE* 1.3 63.3 + - - +
159Y ARG* 3.9 5.1 - - - +
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Residues in contact with ILE 158 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49Y LEU* 3.2 22.4 - - + +
62Y LEU* 3.5 29.4 - - + -
65Y ILE* 5.9 1.3 - - + -
66Y LEU* 4.7 5.2 - - + -
130Y VAL* 3.4 27.1 - - + -
131Y SER 2.7 9.7 + - - +
132Y TRP* 3.3 54.3 - - + +
133Y LEU 4.1 0.3 + - - -
134Y GLU* 4.3 1.0 - - - +
156Y LEU* 4.2 17.0 - - + -
157Y ASN* 1.3 80.0 - - - +
159Y ARG* 1.3 68.2 - - - +
160Y LEU* 3.9 21.1 - - + -
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Residues in contact with ARG 159 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48Y GLU* 3.1 45.1 + - - +
49Y LEU 2.9 6.5 + - - -
50Y SER* 3.3 22.6 + - - +
51Y LEU 2.9 27.5 + - - +
133Y LEU 4.0 6.3 - - - +
134Y GLU* 3.3 24.3 + - + +
136Y LEU* 6.3 0.4 - - - -
141Y ARG* 4.2 5.7 - - - +
157Y ASN* 3.9 7.0 - - - +
158Y ILE* 1.3 78.4 - - - +
160Y LEU* 1.3 65.4 + - - +
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Residues in contact with LEU 160 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51Y LEU* 3.5 34.5 - - + +
58Y CYS* 4.3 15.3 - - + +
59Y LEU* 5.0 15.9 - - + -
62Y LEU* 5.0 6.5 - - + -
84Y PRO* 4.2 25.6 - - + -
86Y SER* 6.2 0.7 - - - -
87Y LEU* 5.0 1.8 - - + -
132Y TRP* 4.4 10.3 - - + +
134Y GLU* 3.6 20.2 + - - +
158Y ILE* 3.9 15.5 - - + -
159Y ARG* 1.3 82.0 - - - +
161Y GLY* 1.3 59.3 + - - +
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Residues in contact with GLY 161 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51Y LEU 3.2 5.6 + - - +
52Y SER* 3.1 16.0 + - - -
53Y GLY 3.1 35.7 + - - +
58Y CYS* 3.8 4.1 - - - -
160Y LEU* 1.3 77.5 - - - +
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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