Contacts of the strand formed by residues 155 - 161 (chain D) in PDB entry 4F2N
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151D ASN* 4.0 2.5 - - - -
153D GLY 4.0 0.8 + - - -
154D SER* 1.3 76.7 - - - +
156D TRP* 1.3 64.7 + - - -
173D THR 3.3 11.9 - - - -
175D ASN 3.5 8.7 - - - -
192D VAL* 2.8 35.2 + - - +
193D TRP* 3.2 19.0 + - - +
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Residues in contact with TRP 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D GLN* 3.0 19.3 + - - -
107D ASN* 3.4 52.4 - - + +
108D HIS* 3.5 30.5 - + - -
111D PHE* 3.9 11.2 - - + -
151D ASN* 3.1 6.9 + - - +
155D GLY* 1.3 80.1 - - - -
157D THR* 1.3 62.9 + - - +
158D TRP* 3.3 25.7 - + + +
172D SER* 3.4 0.2 - - - -
173D THR* 2.9 37.7 + - - +
175D ASN 3.2 16.2 + - - -
177D GLY 4.2 0.2 - - - -
189D THR* 3.4 18.4 - - + -
190D ALA 3.5 6.5 - - - -
191D ASP* 3.4 46.4 - - + -
192D VAL* 4.1 1.1 - - - -
193D TRP* 3.5 5.1 - - - +
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Residues in contact with THR 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144D PHE* 3.2 34.7 - - + +
147D ALA* 3.9 17.9 - - + -
148D GLY* 3.2 27.5 - - - +
151D ASN* 3.8 4.9 + - - -
156D TRP* 1.3 73.5 + - - +
158D TRP* 1.3 62.7 + - - +
170D ILE* 4.2 2.9 - - + -
171D ASP 3.5 5.2 - - - +
172D SER* 3.3 19.8 + - - +
189D THR* 3.2 3.1 + - - -
190D ALA* 2.9 37.1 + - - -
192D VAL* 4.3 3.1 - - - +
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Residues in contact with TRP 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D PHE* 4.3 9.0 - + - -
107D ASN* 3.1 38.6 - - + -
110D PHE* 4.1 9.6 - + - -
144D PHE* 3.8 5.1 - - - -
156D TRP* 3.3 25.7 - - + +
157D THR* 1.3 78.0 - - - +
159D LEU* 1.3 59.4 + - - +
160D CYS* 3.7 16.8 - - - -
169D LEU 3.6 0.2 - - - +
170D ILE* 3.2 10.4 - - - +
171D ASP* 2.6 45.0 + - + +
173D THR* 3.0 24.2 + - + -
177D GLY 3.9 5.6 - - - -
179D PRO* 3.3 30.0 - - + +
186D PRO* 3.6 35.7 - - + -
188D PHE 3.5 5.8 - - - -
189D THR* 3.5 26.9 - - + -
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Residues in contact with LEU 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D ILE* 4.3 20.6 - - + -
134D PHE* 3.9 22.0 - - + -
140D PHE* 3.7 39.9 - - + -
144D PHE* 3.9 4.0 - - + -
158D TRP* 1.3 71.5 - - - +
160D CYS* 1.3 60.9 + - - +
168D LEU* 4.1 12.8 - - + -
169D LEU 3.4 13.2 - - - +
170D ILE* 4.6 0.7 - - + +
186D PRO* 3.7 1.7 - - - +
187D ILE* 2.8 51.7 + - + +
188D PHE* 2.9 26.9 + - + +
218D TRP* 5.3 1.8 - - + -
221D VAL* 4.9 3.4 - - + -
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Residues in contact with CYS 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158D TRP* 3.7 21.8 - - - -
159D LEU* 1.3 79.1 - - - +
161D VAL* 1.3 64.6 + - - +
168D LEU* 3.2 10.4 - - - +
169D LEU* 2.8 36.7 + - + +
171D ASP* 4.6 3.8 - - - -
179D PRO* 3.8 26.5 - - - -
184D LEU* 4.1 21.8 - - + -
185D ARG 3.3 9.6 - - - +
186D PRO* 3.8 15.7 - - - -
187D ILE* 4.3 0.9 - - - +
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Residues in contact with VAL 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160D CYS* 1.3 74.3 - - - +
162D ASP* 1.3 74.2 + - - +
163D PRO* 3.5 5.9 - - + +
166D LYS* 4.6 3.4 - - - +
167D GLU 3.5 6.3 - - - +
168D LEU* 3.7 20.4 - - + -
184D LEU* 3.8 2.5 - - - +
185D ARG* 2.8 37.3 + - + +
187D ILE* 3.9 7.9 - - + -
225D TYR* 3.9 6.7 - - + -
228D ALA* 3.8 32.1 - - + +
229D THR* 3.7 35.4 - - + -
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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