Contacts of the strand formed by residues 169 - 177 (chain B) in PDB entry 3AIH
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 ARG 169 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B ASP* 5.1 10.7 + - - +
154B TRP 3.3 9.1 + - - +
155B ASP* 3.5 39.5 + - - +
167B LEU 3.9 2.1 + - - +
168B LYS* 1.3 83.1 - - - +
170B TYR* 1.3 66.1 + - - +
226B ARG* 3.1 31.7 + - - +
227B LEU* 4.2 39.4 - - + +
228B CYS 5.4 4.5 - - - +
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Residues in contact with TYR 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B PHE* 3.6 36.8 - + - -
153B ASP* 3.6 2.4 - - - +
154B TRP* 2.8 46.6 + - + +
168B LYS* 5.2 5.6 - - + -
169B ARG* 1.3 78.0 - - - +
171B HIS* 1.3 68.7 + - - +
172B SER* 3.6 29.8 + - - -
193B ARG* 5.9 7.5 - - + +
194B PHE 5.4 0.9 - - - -
195B LEU* 6.6 0.2 - - + -
227B LEU* 4.6 5.6 - - - -
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Residues in contact with HIS 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B ALA* 4.2 10.3 - - + +
152B PHE 3.2 7.6 - - - -
153B ASP* 2.9 36.2 + - + +
170B TYR* 1.3 83.7 - - - +
172B SER* 1.3 79.5 + - - +
173B GLN* 3.0 29.3 + - + +
192B VAL 4.1 0.2 - - - +
193B ARG* 4.2 2.1 - - - +
194B PHE* 3.3 60.6 + + + +
227B LEU* 4.4 15.0 - - + +
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Residues in contact with SER 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B ALA* 3.2 2.9 - - - +
152B PHE* 2.8 37.3 + - - +
170B TYR* 3.6 29.1 + - - -
171B HIS* 1.3 78.0 - - - +
173B GLN* 1.3 70.1 + - - +
174B THR* 4.7 7.5 - - - +
191B GLU* 5.1 6.1 + - - +
192B VAL 3.3 10.9 + - - -
193B ARG* 5.5 7.3 + - - -
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Residues in contact with GLN 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B PHE* 3.7 12.5 - - - -
124B TYR* 4.9 6.2 - - - -
125B GLY* 4.2 6.7 + - - +
148B TYR* 4.4 6.0 - - + -
150B SER 3.3 7.6 - - - +
151B ALA* 3.7 13.9 - - + +
171B HIS* 3.0 27.1 + - + +
172B SER* 1.3 81.7 + - - +
174B THR* 1.3 66.9 + - - +
175B TYR* 2.7 41.9 + - + -
191B GLU* 3.5 3.3 - - - +
192B VAL* 2.8 37.1 + - + +
194B PHE* 3.8 14.0 - - + -
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Residues in contact with THR 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A SER* 6.4 0.2 - - - -
149B GLN* 2.9 43.0 + - - -
150B SER* 2.7 36.5 + - - +
172B SER* 4.7 7.2 - - - +
173B GLN* 1.3 80.0 - - - +
175B TYR* 1.3 68.6 + - - +
190B ALA 3.5 7.6 - - - -
191B GLU* 4.0 24.5 - - + +
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Residues in contact with TYR 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B PHE* 3.2 15.3 - + - -
125B GLY* 3.0 19.1 + - - -
126B ARG 4.1 0.2 - - - -
127B HIS* 3.9 15.9 - - - -
128B ILE* 3.8 16.6 - - + -
145B LEU 4.1 0.3 - - - +
146B GLY* 3.9 21.3 - - - -
147B TYR 3.3 6.5 - - - +
148B TYR* 3.4 38.6 - + + -
149B GLN* 4.4 1.8 - - - +
173B GLN* 2.7 41.0 + - + -
174B THR* 1.3 76.4 - - - +
176B GLY* 1.3 59.6 + - - +
189B GLU* 3.4 5.0 - - - +
190B ALA* 2.8 39.5 + - + +
192B VAL* 3.6 30.5 - - + -
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Residues in contact with GLY 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A ARG* 6.5 0.2 - - - -
146B GLY* 3.9 0.4 - - - -
147B TYR* 2.8 34.0 + - - +
149B GLN* 3.7 21.7 - - - +
175B TYR* 1.3 73.3 - - - +
177B ASN* 1.3 72.8 + - - +
178B GLY 3.2 2.9 - - - -
188B ARG 4.0 4.5 - - - -
189B GLU* 4.5 5.6 - - - -
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Residues in contact with ASN 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A ARG* 6.2 2.4 - - - +
147B TYR* 3.4 19.3 - - + -
149B GLN* 4.7 8.6 + - - -
176B GLY* 1.3 75.3 - - - +
178B GLY* 1.3 65.6 + - - +
187B PRO* 3.9 23.6 - - - +
188B ARG 3.5 4.2 + - - -
189B GLU* 5.2 0.4 - - - +
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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