Contacts of the strand formed by residues 155 - 161 (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 GLY 155 (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 5.1 6.8 + - - -
2C NAG 5.8 5.2 - - - -
152U GLY 4.7 0.2 - - - -
153U CYS 2.4 15.0 + - - +
154U PRO* 1.3 70.4 - - - +
156U SER* 1.3 56.8 + - - -
169U LYS* 4.6 0.5 - - - +
170U CYS* 2.7 47.1 + - - +
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Residues in contact with SER 156 (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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152U GLY 4.7 5.2 + - - -
153U CYS 4.9 0.2 - - - -
154U PRO 4.3 0.6 + - - -
155U GLY* 1.3 76.3 - - - -
157U ASN* 1.3 54.7 + - - +
167U PHE* 4.3 15.0 - - - -
168U LEU 3.0 18.8 - - - -
169U LYS* 3.7 16.6 - - - -
243U THR* 5.1 1.6 - - - +
245U SER* 2.7 27.4 + - - -
402U PG4 5.8 3.6 - - - +
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Residues in contact with ASN 157 (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* 5.5 0.2 + - - -
151U PRO 4.6 2.0 + - - -
152U GLY* 3.8 26.3 + - - -
156U SER* 1.3 71.3 - - - +
158U GLY* 1.3 59.2 + - - +
166U HIS* 2.8 34.1 - - - -
167U PHE* 3.3 9.0 - - - -
168U LEU* 2.9 41.1 + - - +
243U THR* 3.4 4.7 - - - +
245U SER* 3.1 22.6 + - - +
246U MET* 3.3 29.7 - - + +
252U LEU 5.7 1.4 - - - +
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Residues in contact with GLY 158 (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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157U ASN* 1.3 78.8 + - - +
159U PHE* 1.3 62.6 + - - +
166U HIS* 3.1 11.4 - - - -
167U PHE* 3.4 15.9 - - - -
219U MET* 3.5 6.7 - - - -
242U ALA* 3.3 2.4 - - - -
243U THR* 3.0 35.7 + - - +
246U MET* 3.4 7.9 - - - +
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Residues in contact with PHE 159 (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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158U GLY* 1.3 76.2 - - - +
160U HIS* 1.3 66.7 + - - +
161U ASN* 3.7 40.8 - - + -
164U THR* 4.5 15.5 - - + -
165U PHE* 3.3 2.1 - - - -
166U HIS* 2.8 42.1 + - + +
219U MET* 3.5 4.9 - - - -
223U LEU* 3.8 17.9 - - + -
238U VAL* 3.8 18.8 - - + -
240U GLY* 3.7 22.2 - - - -
241U CYS 3.1 23.6 - - - -
242U ALA* 4.0 8.5 - - + -
246U MET* 4.5 6.1 - - - -
255U ALA* 6.0 2.0 - - + -
256U PHE* 3.7 32.8 - + + -
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Residues in contact with HIS 160 (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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159U PHE* 1.3 81.7 - - - +
161U ASN* 1.3 63.8 + - - +
164U THR 3.0 15.0 - - - +
165U PHE* 4.0 12.8 - - + -
184U LEU* 4.0 21.8 - - + -
213U ILE* 3.6 9.5 - - + +
214U ASP 3.3 20.9 + - - -
215U CYS* 3.7 1.4 - - - -
216U ARG* 3.1 38.1 + - + +
219U MET* 3.7 19.6 - - + +
240U GLY* 3.7 0.2 - - - -
241U CYS* 3.0 52.1 + - + +
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Residues in contact with ASN 161 (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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159U PHE* 3.7 9.4 - - + -
160U HIS* 1.3 79.5 - - - +
162U ASN* 1.3 60.5 + - - +
163U ASP* 2.6 20.9 + - - +
164U THR* 2.9 37.3 + - - +
196U SER* 3.2 10.8 + - - +
197U CYS 3.6 9.3 + - - -
198U LYS* 4.9 3.2 - - - +
213U ILE* 3.6 12.8 - - - -
238U VAL* 3.5 21.8 - - - +
239U ARG 3.3 23.0 + - - +
240U GLY* 3.9 1.8 - - - -
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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