Contacts of the strand formed by residues 127 - 134 (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 HIS 127 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B VAL 3.6 1.0 - - - +
78B PHE 3.8 0.2 - - - -
79B LEU* 2.8 43.4 + - + +
80B PRO 3.7 19.7 - - - +
81B GLN* 3.5 13.1 + - - +
86B ARG* 3.3 42.2 + - - +
109B GLU* 3.6 30.7 + - + -
125B GLN* 5.0 1.1 + - - +
126B PRO* 1.3 72.9 - - - +
128B ILE* 1.3 62.3 + - - +
129B GLU* 2.8 43.0 + - + +
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Residues in contact with ILE 128 (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* 3.6 34.1 - - + -
77B VAL 3.5 9.0 - - - +
78B PHE* 3.9 22.4 - - + -
109B GLU* 4.4 3.5 - - - +
110B VAL* 3.3 32.0 + - + +
112B VAL* 4.3 5.8 - - + -
125B GLN* 4.1 8.8 - - + +
126B PRO* 3.7 9.4 + - + +
127B HIS* 1.3 78.9 + - - +
129B GLU* 1.3 65.8 + - - +
187B PHE* 3.7 30.1 - - + -
188B TYR* 3.6 22.0 - - + +
215B TRP* 4.4 7.0 - - + -
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Residues in contact with GLU 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B MET* 3.9 1.0 - - - +
77B VAL* 2.8 36.2 + - - +
79B LEU* 4.2 6.0 - - + +
86B ARG* 4.3 1.2 + - - -
90B ARG* 2.7 44.1 + - - -
107B TRP* 3.5 27.2 - - + +
108B ARG 3.4 12.5 - - - +
109B GLU* 4.2 13.6 + - - +
110B VAL* 4.0 2.5 - - - -
127B HIS* 2.8 34.8 + - + +
128B ILE* 1.3 78.2 - - - +
130B GLN* 1.3 63.5 + - - +
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Residues in contact with GLN 130 (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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51B PRO* 5.9 0.4 - - - +
55B LEU* 3.8 10.4 - - - +
74B VAL* 4.2 10.3 - - + -
75B GLY 3.0 9.6 - - - +
76B MET* 3.6 27.4 - - - -
107B TRP* 3.2 8.0 - - - -
108B ARG* 2.8 70.2 + - + +
110B VAL* 3.5 12.1 - - + +
129B GLU* 1.3 72.9 - - - +
131B ILE* 1.3 61.0 + - - +
132B LEU* 4.1 3.0 + - + +
173B ILE* 3.6 16.6 - - + +
175B TYR* 2.8 34.8 + - - -
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Residues in contact with ILE 131 (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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73B GLY 3.7 1.2 - - - +
74B VAL* 3.3 7.4 - - - +
75B GLY* 2.9 43.3 + - - +
77B VAL* 4.3 10.5 - - + -
93B VAL* 3.9 15.0 - - + -
94B GLU* 4.3 2.7 - - + -
97B VAL* 4.4 3.6 - - + -
104B VAL* 3.9 31.9 - - + -
106B GLY 3.7 7.4 - - - +
107B TRP* 3.6 39.9 - - + +
130B GLN* 1.3 72.8 - - - +
132B LEU* 1.3 64.0 + - - +
133B VAL* 4.0 10.1 - - + -
168B PHE* 3.7 23.7 - - + -
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Residues in contact with LEU 132 (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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55B LEU* 4.2 18.4 - - + -
58B TRP* 3.3 50.9 - - + +
59B PHE* 4.0 7.2 - - + -
72B LEU* 4.2 15.5 - - + -
73B GLY 3.5 1.6 - - - -
74B VAL* 3.8 36.6 - - + -
104B VAL* 3.7 1.2 - - - -
105B LEU* 2.8 42.9 + - + -
106B GLY 2.9 13.2 + - - +
108B ARG* 4.6 7.2 - - + -
130B GLN* 4.7 5.8 - - + +
131B ILE* 1.3 74.8 - - - +
133B VAL* 1.3 59.0 + - - +
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Residues in contact with VAL 133 (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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72B LEU* 3.6 3.1 - - - +
73B GLY* 2.8 38.5 + - - +
97B VAL* 3.7 22.0 - - + -
102B LEU* 4.0 31.9 - - + -
103B THR 3.2 11.2 - - - +
104B VAL* 4.3 2.0 - - - -
105B LEU 4.5 0.7 - - - +
131B ILE* 4.0 14.1 - - + -
132B LEU* 1.3 78.7 - - - +
134B THR* 1.3 75.3 + - - +
144B LEU* 4.9 1.6 - - + -
148B LEU* 4.2 11.7 - - + -
168B PHE* 3.9 19.1 - - + -
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Residues in contact with THR 134 (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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67B PRO* 3.4 34.8 - - + -
71B ARG* 3.8 12.6 - - - +
73B GLY 5.1 0.2 - - - +
102B LEU* 3.4 10.3 - - - +
103B THR* 2.8 43.0 + - - +
105B LEU* 3.6 27.6 - - + +
133B VAL* 1.3 80.3 - - - +
135B CYS* 1.3 62.8 + - - +
136B PRO* 3.7 2.1 - - - +
144B LEU* 5.2 2.2 - - - -
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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