Contacts of the strand formed by residues 143 - 149 (chain U) in PDB entry 2FD6
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 143 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99U GLY* 3.5 2.4 - - - -
100U SER* 2.5 38.3 + - - +
105U CYS* 3.9 20.6 - - + -
106U GLU* 3.9 17.3 - - + -
124U ASP* 5.7 0.6 + - - -
125U VAL 3.6 1.8 - - - -
126U VAL* 3.5 21.9 - - + +
128U HIS* 3.1 23.1 + + - -
142U ARG* 1.3 81.2 + - + +
144U LEU* 1.3 68.1 + - - +
145U ARG* 6.4 0.2 - - + -
181U ILE* 3.6 26.2 - - + +
182U LEU 3.3 20.9 - - - -
183U GLU* 2.6 27.1 + - - -
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Residues in contact with LEU 144 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A ASN* 3.8 11.9 - - - +
55U LEU* 3.8 27.6 - - + -
57U TYR* 3.9 36.8 - - + +
98U CYS 3.9 2.5 - - - -
99U GLY* 4.2 5.8 - - - -
105U CYS* 4.8 0.2 - - - -
123U LEU 4.1 0.2 - - - +
124U ASP* 3.5 1.4 + - - +
125U VAL* 2.8 54.6 + - + +
141U ASP* 3.3 40.4 - - + +
143U HIS* 1.3 82.9 - - - +
145U ARG* 1.3 65.5 + - - +
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Residues in contact with ARG 145 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55U LEU* 5.5 1.8 - - - -
57U TYR* 3.2 10.2 - - - +
96U ILE* 3.6 18.0 - - - +
97U SER* 2.5 29.7 + - - -
98U CYS* 3.2 34.3 + - - +
105U CYS* 4.8 0.9 - - - -
110U HIS* 3.2 22.2 + - - -
123U LEU* 3.4 7.6 - - - +
124U ASP* 2.8 30.1 + - - +
143U HIS* 6.4 0.2 - - + -
144U LEU* 1.3 79.4 - - - +
146U GLY* 1.3 53.3 + - - +
177U ASN 3.2 24.6 + - - -
178U GLU* 3.5 4.9 + - - +
179U GLY 2.8 38.3 + - - +
180U PRO 3.1 21.0 + - - -
181U ILE* 3.5 11.6 - - - +
182U LEU 4.7 0.4 - - - +
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Residues in contact with GLY 146 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55U LEU* 5.1 1.9 - - - +
56U SER 3.2 11.0 - - - -
95U CYS* 3.8 4.6 - - - +
96U ILE 3.4 11.4 + - - -
97U SER* 3.7 7.2 - - - -
113U LEU* 4.6 1.3 - - - -
122U CYS* 3.5 6.6 - - - -
123U LEU* 2.9 34.6 + - - +
145U ARG* 1.3 76.3 - - - +
147U CYS* 1.3 64.6 + - - -
177U ASN* 3.6 2.6 - - - +
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Residues in contact with CYS 147 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55U LEU* 3.1 9.0 - - - +
56U SER* 2.7 37.4 + - - +
95U CYS* 4.1 2.2 - - - -
113U LEU* 3.4 25.1 - - + +
115U CYS* 2.0 58.8 - - - -
120U GLU* 3.2 13.5 - - - +
121U GLN 3.5 5.4 - - - -
123U LEU* 4.0 2.7 - - - -
146U GLY* 1.3 75.5 - - - -
148U GLY* 1.3 58.7 + - - +
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Residues in contact with GLY 148 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54U THR 3.1 16.6 - - - -
55U LEU 4.1 0.2 - - - -
120U GLU* 3.4 20.6 - - - +
121U GLN* 2.7 38.0 + - - +
123U LEU* 3.5 10.4 - - - +
147U CYS* 1.3 79.6 - - - +
149U TYR* 1.3 60.7 + - - +
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Residues in contact with TYR 149 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52U ASN 4.5 13.0 - - - -
53U ARG* 3.2 9.0 - - - +
54U THR* 2.9 35.2 + - - +
119U GLU* 3.6 26.7 - - + +
120U GLU* 5.0 2.7 - - + -
121U GLN* 3.2 27.8 - - - -
123U LEU* 3.7 0.8 - - - +
148U GLY* 1.3 74.8 - - - +
150U LEU* 1.3 71.3 + - - +
151U PRO* 6.1 0.2 - - + -
153U CYS* 3.8 16.2 - - + -
154U PRO* 3.5 21.2 - - + +
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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