Contacts of the strand formed by residues 121 - 128 (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 GLN 121 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1C NAG 5.2 1.6 + - - -
93U LEU* 4.1 4.5 - - - -
95U CYS* 4.1 4.5 - - - -
119U GLU 3.9 7.2 + - - +
120U GLU* 1.3 76.5 - - - +
122U CYS* 1.3 64.5 + - - +
123U LEU* 3.6 0.9 + - - +
147U CYS* 3.5 5.5 - - - -
148U GLY 2.7 28.9 + - - +
149U TYR* 3.2 30.6 - - + -
153U CYS* 4.3 1.0 - - - +
154U PRO* 4.3 13.5 - - - +
170U CYS* 3.4 29.3 - - - +
171U CYS* 3.2 26.2 - - - +
172U ASN* 3.6 22.4 + - + +
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Residues in contact with CYS 122 (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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93U LEU* 3.8 12.8 - - - -
94U GLU 3.7 7.9 - - - -
95U CYS* 2.0 52.9 - - - -
121U GLN* 1.3 71.4 - - - +
123U LEU* 1.3 61.3 + - - +
169U LYS 3.6 0.9 - - - +
170U CYS* 3.3 5.9 - - - -
171U CYS* 2.9 28.7 + - - -
173U THR 3.9 2.0 - - - -
175U LYS 4.1 2.0 - - - -
176U CYS* 3.4 29.2 - - - -
177U ASN* 3.5 16.1 - - + +
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Residues in contact with LEU 123 (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 4.1 0.2 - - - +
55U LEU* 3.9 18.6 - - + -
121U GLN 3.7 7.2 - - - +
122U CYS* 1.3 79.4 - - - +
124U ASP* 1.3 63.2 + - - +
125U VAL* 4.2 3.1 - - + +
144U LEU 4.5 0.2 - - - -
145U ARG* 3.4 4.2 - - - +
146U GLY 2.9 27.3 + - - +
147U CYS 3.9 5.8 - - - +
148U GLY* 3.5 34.3 - - - +
149U TYR 3.7 2.9 - - - +
150U LEU* 4.1 18.4 - - + -
153U CYS* 3.3 32.5 - - - -
168U LEU* 4.4 8.5 - - + -
169U LYS 3.3 2.7 - - - +
170U CYS* 3.4 15.5 - - + -
177U ASN* 3.1 16.3 - - - +
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Residues in contact with ASP 124 (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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123U LEU* 1.3 76.4 - - - +
125U VAL* 1.3 61.4 + - - +
126U VAL* 4.3 15.6 - - - +
143U HIS* 5.7 0.7 + - - +
144U LEU 3.5 4.0 - - - +
145U ARG* 2.8 42.2 + - - +
167U PHE* 3.6 2.4 - - - +
168U LEU* 3.4 3.2 - - - -
169U LYS* 2.8 53.7 + - + +
177U ASN* 3.5 15.2 - - + +
178U GLU 5.2 0.2 - - - +
181U ILE* 5.9 0.5 - - - +
182U LEU* 5.4 6.5 + - - +
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Residues in contact with VAL 125 (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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23A LYS* 4.6 2.9 - - - +
24A TYR* 4.2 26.5 - - + +
55U LEU* 5.0 12.6 - - + -
123U LEU* 5.6 2.2 - - + -
124U ASP* 1.3 76.8 + - - +
126U VAL* 1.3 65.4 + - - +
127U THR* 3.9 17.2 + - - +
141U ASP 5.2 0.5 - - - +
142U ARG 3.7 0.7 - - - +
143U HIS* 3.6 3.6 - - - -
144U LEU* 2.8 69.1 + - + +
150U LEU* 5.3 5.8 - - + -
166U HIS* 4.9 1.6 - - - +
167U PHE 3.3 8.1 - - - +
168U LEU* 4.8 10.5 - - + -
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Residues in contact with VAL 126 (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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124U ASP* 4.3 12.3 - - - +
125U VAL* 1.3 75.9 - - - +
127U THR* 1.3 63.9 + - - +
128U HIS* 3.5 28.5 - - + -
142U ARG 3.3 2.7 - - - -
143U HIS* 3.5 22.4 - - + +
165U PHE* 3.7 22.2 - - + +
166U HIS* 3.3 10.7 - - - +
167U PHE* 2.8 43.7 + - + +
182U LEU* 3.7 22.7 - - + +
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Residues in contact with THR 127 (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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23A LYS* 3.0 42.7 + - + +
125U VAL* 3.9 7.7 + - - +
126U VAL* 1.3 74.5 - - - +
128U HIS* 1.3 63.0 + - - +
129U TRP* 3.8 2.6 + - - +
140U ASP* 4.5 16.6 - - - +
141U ASP 3.7 15.2 + - - +
142U ARG* 2.7 33.8 + - - +
165U PHE 4.0 1.8 - - - -
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Residues in contact with HIS 128 (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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126U VAL* 3.5 27.1 - - + -
127U THR* 1.3 75.1 - - - +
129U TRP* 1.3 72.0 + - - +
142U ARG* 2.6 40.8 + - + +
143U HIS* 3.1 15.1 + + - -
164U THR* 3.8 3.3 - - - +
165U PHE* 3.1 47.4 + + + +
183U GLU* 2.9 27.0 + - - -
184U LEU 5.7 0.2 - - - -
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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