Contacts of the strand formed by residues 73 - 79 (chain A) in PDB entry 1OFD
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 GLY 73 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A ARG 3.8 2.0 + - - -
72A LEU* 1.3 75.5 - - - +
74A VAL* 1.3 62.8 + - - +
75A GLY 4.3 0.2 - - - -
131A ILE 3.7 0.2 - - - +
132A LEU* 3.6 3.1 - - - -
133A VAL* 2.8 41.3 + - - -
144A LEU* 4.2 3.7 - - - +
148A LEU* 4.1 20.0 - - - -
168A PHE* 4.4 5.4 - - - -
169A SER 3.7 6.7 - - - -
170A CYS* 4.2 1.8 - - - -
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Residues in contact with VAL 74 (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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50A ILE* 4.1 18.4 - - + -
55A LEU* 3.8 20.9 - - + -
72A LEU* 4.1 12.8 - - + +
73A GLY* 1.3 79.1 - - - +
75A GLY* 1.3 61.9 + - - +
76A MET 4.1 0.3 + - - -
130A GLN* 4.1 14.6 - - + -
131A ILE 3.4 2.7 - - - +
132A LEU* 3.8 26.7 - - + -
167A SER* 3.7 2.9 + - - +
168A PHE* 3.4 6.2 + - - -
169A SER 2.9 31.7 + - - +
172A THR 4.8 3.7 - - - +
173A ILE* 3.8 28.4 - - + +
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Residues in contact with GLY 75 (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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74A VAL* 1.3 73.6 - - - +
76A MET* 1.3 61.5 + - - -
77A VAL* 3.7 7.7 + - - +
130A GLN* 3.0 9.5 - - - -
131A ILE* 2.8 45.0 + - - -
167A SER 3.2 8.3 - - - -
168A PHE* 3.5 17.9 - - - -
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Residues in contact with MET 76 (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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74A VAL* 4.1 1.2 - - - +
75A GLY* 1.3 70.7 - - - -
77A VAL* 1.3 58.4 + - - +
78A PHE* 5.2 0.9 - - + -
110A VAL* 4.0 2.9 - - + -
128A ILE* 3.7 32.1 - - + -
129A GLU 3.9 0.7 - - - -
130A GLN* 3.5 25.4 - - - +
165A VAL* 3.7 3.1 - - - -
166A CYS* 2.9 39.3 + - + +
167A SER* 2.9 27.0 + - - +
173A ILE* 4.1 10.1 - - + -
174A VAL 3.3 21.5 - - - +
175A TYR* 3.7 35.2 - - + -
188A TYR* 3.7 15.7 - - + +
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Residues in contact with VAL 77 (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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75A GLY* 3.7 16.6 - - - +
76A MET* 1.3 79.6 - - - +
78A PHE* 1.3 78.5 + - - +
79A LEU* 3.8 21.7 - - + +
93A VAL* 4.6 11.9 - - + -
107A TRP* 4.1 21.5 - - + -
127A HIS 3.6 0.9 - - - +
128A ILE* 3.5 5.4 - - - +
129A GLU 2.8 37.3 + - - +
131A ILE* 4.3 8.3 - - + -
163A PHE* 4.7 3.4 - - + -
164A TYR 3.7 8.7 - - - +
165A VAL* 4.4 21.1 - - + -
168A PHE* 6.2 0.4 - - + -
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Residues in contact with PHE 78 (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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76A MET* 5.2 2.7 - - + -
77A VAL* 1.3 79.9 - - - +
79A LEU* 1.3 60.4 + - - +
126A PRO* 3.6 20.6 - - + -
127A HIS 3.7 2.7 - - - -
128A ILE* 3.7 28.5 - - + -
161A GLU 5.2 1.3 - - - +
162A ASP 3.8 4.3 - - - +
163A PHE* 3.3 5.7 - - - -
164A TYR* 2.8 55.3 + + + +
166A CYS* 3.3 26.5 - - - -
176A LYS* 3.6 24.5 - - + -
188A TYR* 3.8 15.3 - - - -
215A TRP* 3.7 40.2 - + + -
216A PRO* 4.1 4.9 - - + -
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Residues in contact with LEU 79 (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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77A VAL* 3.8 22.2 - - + +
78A PHE* 1.3 73.3 - - - +
80A PRO* 1.3 67.9 - - + +
81A GLN 3.5 0.3 + - - -
86A ARG* 4.2 17.5 - - + +
89A ALA* 3.8 25.1 - - + -
90A ARG* 4.1 19.3 - - + +
93A VAL* 4.9 0.4 - - + -
107A TRP* 4.0 23.8 - - + -
126A PRO* 3.6 5.2 - - - +
127A HIS* 2.6 45.8 + - + +
129A GLU* 4.1 30.5 - - + +
162A ASP* 3.0 7.3 - - - +
163A PHE* 4.2 7.0 - - + -
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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