Contacts of the strand formed by residues 164 - 171 (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 THR 164 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128U HIS 3.8 5.6 - - - +
129U TRP 3.7 7.9 + - - +
159U PHE* 4.5 14.4 - - + -
160U HIS* 3.0 7.1 - - - +
161U ASN* 2.9 40.9 + - - +
163U ASP* 1.3 98.9 + - - +
165U PHE* 1.3 73.1 + - - +
166U HIS* 4.4 7.0 - - + +
184U LEU* 5.0 2.0 - - - +
255U ALA 5.1 7.6 - - - +
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Residues in contact with PHE 165 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126U VAL* 3.6 30.4 - - + +
127U THR* 4.0 0.2 - - - -
128U HIS* 3.1 46.5 + + + +
159U PHE 3.3 10.1 - - - -
160U HIS* 4.0 1.8 - - + -
164U THR* 1.3 79.4 - - - +
166U HIS* 1.3 75.8 + - - +
167U PHE* 3.9 22.0 - + + -
182U LEU* 3.5 28.7 - - + -
183U GLU 4.0 1.1 - - - -
184U LEU* 3.5 58.1 - - + -
187U LEU* 4.3 4.7 - - + -
219U MET* 4.1 8.5 - - + -
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Residues in contact with HIS 166 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LYS* 2.8 33.2 - - - +
24A TYR* 3.1 25.0 + - - -
125U VAL* 4.9 1.9 - - + +
126U VAL 3.3 6.3 - - - +
127U THR* 5.5 0.4 - - - -
157U ASN* 2.8 31.2 + - - -
158U GLY* 3.1 5.9 - - - -
159U PHE* 2.8 46.2 + - + +
164U THR* 4.4 7.1 - - + +
165U PHE* 1.3 79.1 - - - +
167U PHE* 1.3 71.2 + - - +
168U LEU* 4.0 9.2 - - + +
246U MET* 4.7 4.3 - - + -
255U ALA* 3.6 31.7 - - + +
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Residues in contact with PHE 167 (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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406H PGE 4.3 17.0 - - - -
124U ASP 3.6 2.1 - - - +
125U VAL* 3.3 4.9 - - - +
126U VAL* 2.8 45.2 + - + +
156U SER* 4.3 16.2 - - - -
157U ASN 3.3 7.4 - - - -
158U GLY* 3.4 24.5 - - - -
165U PHE* 3.9 26.0 - + + -
166U HIS* 1.3 77.7 - - - +
168U LEU* 1.3 82.8 + - - +
169U LYS* 4.7 8.5 - - + -
182U LEU* 3.6 28.9 - - + -
187U LEU* 5.1 1.6 - - + -
218U PRO* 4.3 22.7 - - + -
219U MET* 4.5 5.8 - - + -
243U THR* 4.4 4.0 - - + -
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Residues in contact with LEU 168 (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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24A TYR* 3.7 18.2 - - + +
123U LEU* 4.4 11.4 - - + -
124U ASP 3.4 8.7 - - - +
125U VAL* 4.5 8.5 - - + +
150U LEU* 4.4 15.7 - - + -
151U PRO 3.5 24.2 - - - +
152U GLY 4.0 16.4 - - - +
153U CYS* 4.7 1.3 - - - +
155U GLY 5.6 0.2 - - - +
156U SER* 3.0 6.2 - - - -
157U ASN* 2.9 47.9 + - - +
166U HIS* 4.1 6.3 - - + +
167U PHE* 1.3 77.8 - - - +
169U LYS* 1.3 94.8 + - - +
170U CYS* 4.1 8.7 - - + +
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Residues in contact with LYS 169 (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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122U CYS 3.6 0.7 - - - +
123U LEU* 3.3 5.9 - - - -
124U ASP* 2.8 51.8 + - + +
155U GLY 4.6 0.7 - - - +
156U SER* 3.7 14.1 - - - -
167U PHE* 4.8 9.6 - - + -
168U LEU* 1.3 76.7 - - - +
170U CYS* 1.3 63.7 - - - +
171U CYS* 3.9 19.0 - - - -
176U CYS* 2.6 30.2 + - - +
177U ASN* 4.4 5.1 - - + +
178U GLU 5.2 2.6 + - - -
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Residues in contact with CYS 170 (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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1C NAG 5.2 1.4 + - - -
121U GLN* 3.4 27.3 - - - +
122U CYS 3.3 3.8 - - - -
123U LEU* 3.4 10.5 - - + -
153U CYS* 2.0 68.4 - - - +
155U GLY* 2.7 37.3 + - - +
168U LEU* 4.1 4.0 - - + +
169U LYS* 1.3 75.5 - - - +
171U CYS* 1.3 61.5 + - - +
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Residues in contact with CYS 171 (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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1C NAG 5.1 4.9 - - - +
121U GLN* 3.2 10.7 + - - +
122U CYS* 2.9 33.1 + - - -
169U LYS* 3.9 19.7 - - - -
170U CYS* 1.3 75.4 - - - +
172U ASN* 1.3 60.5 + - - +
173U THR* 4.8 1.6 - - + +
176U CYS* 2.0 62.5 - - + -
177U ASN* 4.0 2.7 - - - -
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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