Contacts of the strand formed by residues 172 - 180 (chain D) in PDB entry 3H2U
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 SER 172 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D ARG* 4.0 3.1 - - - +
139D LEU* 5.2 0.5 - - - +
140D PRO 4.5 2.8 + - - -
141D PRO* 3.5 30.8 + - - +
143D LEU* 4.2 13.8 + - - +
163D LEU* 4.1 18.7 - - - +
164D VAL 3.7 3.8 + - - -
165D TYR* 3.5 24.6 - - - -
171D GLN* 1.3 76.6 - - - +
173D LYS* 1.3 57.7 + - - +
174D GLY* 3.1 20.0 + - - -
175D TYR 4.5 0.2 + - - -
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Residues in contact with LYS 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141D PRO* 6.2 0.4 - - - -
164D VAL* 2.8 25.1 + - + +
165D TYR 4.0 8.3 - - - -
166D SER* 4.1 11.7 - - - +
171D GLN 4.2 0.7 - - - +
172D SER* 1.3 70.5 - - - +
174D GLY* 1.3 59.6 + - - +
175D TYR* 3.4 26.5 - - + +
219D HIS* 3.0 46.9 + - - +
220D SER 4.4 1.8 + - - -
272D ALA 4.1 8.1 + - - -
276D GLU* 3.5 22.8 + - - -
295D SER* 5.6 0.5 - - - -
296D PHE* 3.3 71.4 + - + +
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Residues in contact with GLY 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138D ASN* 3.0 12.1 + - - -
139D LEU* 2.9 48.8 + - - +
141D PRO* 4.8 6.7 - - - -
172D SER* 3.1 14.7 + - - -
173D LYS* 1.3 78.8 - - - +
175D TYR* 1.3 59.7 + - - +
295D SER* 6.4 1.3 - - - -
296D PHE 5.6 0.4 - - - -
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Residues in contact with TYR 175 (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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135D CYS* 4.2 4.9 - - - -
136D VAL 3.2 14.4 - - - +
137D ALA* 3.6 15.0 - - + -
139D LEU* 3.7 7.5 - - - +
163D LEU* 3.7 5.0 - - - +
164D VAL* 3.2 44.3 + - + +
172D SER* 4.5 0.8 + - - -
173D LYS* 3.5 26.9 - - + +
174D GLY* 1.3 80.6 + - - +
176D GLY* 1.3 60.4 + - - +
177D PHE* 4.1 6.3 - + - -
218D LEU 2.8 28.8 + - - -
219D HIS* 3.5 3.5 - - - -
220D SER* 2.9 18.0 + - - -
296D PHE* 3.5 29.8 - + + -
297D CYS 3.9 13.0 - - - -
299D PRO* 3.7 20.9 - - + -
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Residues in contact with GLY 176 (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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135D CYS* 3.2 7.4 - - - -
136D VAL 2.8 29.1 + - - -
139D LEU* 4.0 1.4 - - - +
148D PHE* 3.5 17.7 - - - -
162D PHE 3.2 13.9 - - - -
163D LEU* 3.9 2.9 - - - -
175D TYR* 1.3 76.4 - - - +
177D PHE* 1.3 69.7 + - - -
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Residues in contact with PHE 177 (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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133D LEU* 3.9 15.7 - - + -
134D LEU 3.2 15.3 - - - +
135D CYS* 3.8 15.7 - - + -
136D VAL 4.9 0.4 - - - +
148D PHE* 3.5 6.7 - - - -
160D ARG 4.8 0.2 - - - -
161D CYS* 3.4 4.2 - - - -
162D PHE* 2.9 63.8 + + + -
164D VAL* 3.6 24.2 - - + -
175D TYR* 4.1 11.7 - + - -
176D GLY* 1.3 77.4 - - - -
178D ALA* 1.3 60.9 + - - +
208D THR* 4.2 9.4 - - + -
213D LEU* 3.1 32.8 - - + -
218D LEU* 4.2 6.3 - - + -
299D PRO* 3.6 28.9 - - + -
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Residues in contact with ALA 178 (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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132D ALA 3.4 2.8 - - - +
133D LEU* 3.6 2.2 - - - -
134D LEU* 2.8 38.8 + - + +
136D VAL* 5.4 1.7 - - + +
148D PHE* 4.9 1.8 - - + -
152D VAL* 3.5 42.0 - - + -
158D LEU* 3.9 6.1 - - + -
160D ARG 3.7 5.2 - - - -
161D CYS* 5.2 0.2 - - - -
177D PHE* 1.3 76.0 - - - +
179D GLU* 1.3 59.0 + - - +
180D TYR* 4.1 10.8 - - + -
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Residues in contact with GLU 179 (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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58D ARG* 4.6 7.1 + - - -
129D PRO 5.1 0.5 - - - +
130D THR* 4.1 7.8 + - - -
131D ASP* 3.8 21.8 + - - +
132D ALA 3.1 13.4 + - - +
133D LEU* 3.5 14.3 - - + +
158D LEU* 3.4 4.2 - - - +
159D GLU* 2.6 42.9 + - + +
160D ARG* 2.7 64.3 + - + +
178D ALA* 1.3 73.2 - - - +
180D TYR* 1.3 67.1 + - - +
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Residues in contact with TYR 180 (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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60D LYS* 5.4 0.9 - - - -
131D ASP* 6.0 0.5 - - - +
132D ALA* 3.2 17.3 + - + +
134D LEU* 4.3 4.5 - - + -
152D VAL* 2.6 40.3 + - - +
155D PHE* 3.6 5.2 - - + -
156D GLY 3.3 32.1 - - - -
157D SER 3.3 8.3 - - - +
158D LEU* 3.9 11.0 - - + -
159D GLU* 3.6 11.1 - - - +
178D ALA* 4.1 19.1 - - + -
179D GLU* 1.3 85.3 - - - +
181D MET* 1.3 63.8 + - - +
182D LYS 3.3 20.2 - - - +
185D SER* 3.6 17.0 - - - -
186D ALA* 3.6 24.2 - - - -
189D ALA* 3.4 24.8 - - + +
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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