Contacts of the strand formed by residues 73 - 79 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B ARG 3.9 2.0 + - - -
72B LEU* 1.3 72.8 - - - +
74B VAL* 1.3 61.8 + - - +
131B ILE 3.7 0.7 - - - +
132B LEU* 3.5 4.3 - - - -
133B VAL* 2.8 42.1 + - - +
144B LEU* 4.1 4.8 - - - +
148B LEU* 4.1 20.9 - - - -
168B PHE* 4.4 5.2 - - - -
169B SER 3.8 6.7 - - - -
170B CYS* 4.2 1.8 - - - -
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Residues in contact with VAL 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B ILE* 4.1 19.5 - - + -
55B LEU* 4.0 19.3 - - + -
72B LEU* 4.0 14.4 - - + +
73B GLY* 1.3 79.5 - - - +
75B GLY* 1.3 61.4 + - - +
76B MET 4.2 0.3 + - - -
130B GLN* 4.2 14.6 - - + -
131B ILE 3.3 3.6 - - - +
132B LEU* 3.8 26.9 - - + -
167B SER* 3.8 2.8 + - - +
168B PHE* 3.3 6.6 - - - -
169B SER 2.9 30.5 + - - +
172B THR 4.7 3.5 - - - +
173B ILE* 4.0 24.8 - - + +
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Residues in contact with GLY 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B VAL* 1.3 77.6 - - - +
76B MET* 1.3 60.6 + - - -
77B VAL* 3.7 7.6 - - - +
130B GLN* 3.0 8.3 - - - +
131B ILE* 2.9 43.5 + - - -
165B VAL* 5.0 0.4 - - - -
167B SER 3.2 8.5 - - - -
168B PHE* 3.4 17.1 - - - -
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Residues in contact with MET 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B VAL* 4.2 1.0 - - - +
75B GLY* 1.3 70.3 - - - -
77B VAL* 1.3 59.5 + - - +
78B PHE* 5.2 0.7 - - + -
110B VAL* 4.1 2.7 - - + -
128B ILE* 3.6 30.1 - - + -
129B GLU 4.0 0.7 - - - +
130B GLN* 3.6 26.7 - - - +
165B VAL* 3.6 2.6 - - - +
166B CYS* 2.8 41.6 + - + +
167B SER* 2.9 27.1 + - - +
173B ILE* 4.1 9.6 - - + +
174B VAL 3.2 21.1 - - - +
175B TYR* 3.8 35.4 - - + -
176B LYS 5.5 0.2 - - - +
188B TYR* 3.9 14.1 - - + +
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Residues in contact with VAL 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B GLY* 3.7 16.8 - - - +
76B MET* 1.3 79.4 - - - +
78B PHE* 1.3 72.1 + - - +
79B LEU* 3.7 28.1 + - + +
93B VAL* 4.6 11.4 - - + -
107B TRP* 3.9 23.6 - - + -
127B HIS 3.6 0.9 - - - +
128B ILE* 3.5 7.1 - - - +
129B GLU 2.8 36.5 + - - +
131B ILE* 4.3 7.6 - - + -
163B PHE* 4.8 3.1 - - + -
164B TYR 3.7 7.6 - - - +
165B VAL* 4.2 20.2 - - + +
168B PHE* 6.3 0.4 - - + -
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Residues in contact with PHE 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B MET* 5.2 2.5 - - + -
77B VAL* 1.3 83.3 - - - +
79B LEU* 1.3 59.9 + - - +
126B PRO* 3.7 15.3 - - + -
127B HIS 3.8 2.7 - - - -
128B ILE* 3.9 25.4 - - + -
161B GLU 5.2 1.3 - - - +
162B ASP 3.6 4.3 - - - +
163B PHE* 3.2 5.9 - - - -
164B TYR* 2.7 59.0 + + + +
166B CYS* 3.5 25.1 - - - -
176B LYS* 3.5 25.1 - - + -
188B TYR* 3.8 14.1 - - - -
215B TRP* 3.6 48.9 - + + -
216B PRO* 4.1 6.1 - - + -
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Residues in contact with LEU 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B VAL* 3.7 23.8 - - + -
78B PHE* 1.3 74.8 - - - +
80B PRO* 1.3 73.4 - - + +
81B GLN 3.6 0.2 + - - -
86B ARG* 4.2 14.6 - - + +
89B ALA* 3.9 24.5 - - + -
90B ARG* 4.2 17.3 - - - +
93B VAL* 4.9 0.2 - - + -
107B TRP* 4.3 13.7 - - + -
126B PRO* 3.5 5.9 - - - +
127B HIS* 2.8 42.2 + - + +
129B GLU* 4.2 35.4 - - + +
162B ASP* 2.9 7.0 - - - +
163B PHE* 4.3 6.1 - - + +
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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