Contacts of the strand formed by residues 157 - 164 (chain B) in PDB entry 1IVH
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 HIS 157 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153B LYS* 3.4 8.0 - - - +
154B LYS 2.8 32.7 + - - +
155B GLY 3.2 0.4 - - - -
156B ASN* 1.3 91.3 + - + +
158B TYR* 1.3 68.6 + - - +
159B ILE* 4.9 2.0 - - + -
230B LYS* 3.5 41.1 + - + +
231B ILE 3.1 6.5 - - - +
232B PRO* 3.4 32.6 - - + +
233B ALA 4.1 0.7 - - - +
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Residues in contact with TYR 158 (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 3.7 18.4 - - - +
152B GLU 3.3 6.1 - - - +
153B LYS* 3.7 31.8 + - + +
157B HIS* 1.3 81.4 - - - +
159B ILE* 1.3 62.2 + - - +
160B LEU* 3.8 9.4 + - + -
182B THR* 3.8 11.4 - - + -
196B PHE* 3.6 31.2 - + + -
229B CYS 3.2 2.8 - - - +
230B LYS* 3.4 2.3 - - - -
231B ILE* 2.7 40.3 + - + +
233B ALA* 3.7 30.2 - - + +
236B ILE* 4.2 14.2 - - + +
240B GLU* 3.2 39.7 + - + +
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Residues in contact with ILE 159 (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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150B LYS 3.5 1.2 - - - +
152B GLU* 2.7 61.1 + - + +
154B LYS* 3.7 32.5 - - + +
157B HIS* 4.9 0.9 - - + -
158B TYR* 1.3 81.0 - - - +
160B LEU* 1.3 57.4 + - - +
161B ASN* 3.5 11.9 - - - +
228B ASP* 3.4 38.1 - - + +
229B CYS 3.6 1.8 - - - -
230B LYS* 3.4 39.9 - - + +
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Residues in contact with LEU 160 (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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149B LEU* 3.9 15.0 - - + -
150B LYS 3.2 3.1 - - - +
151B ALA* 3.4 30.7 - - + -
158B TYR* 4.3 11.7 - - + -
159B ILE* 1.3 74.8 - - - +
161B ASN* 1.3 60.2 + - - +
178B VAL* 4.6 10.5 - - + -
180B ALA* 4.4 9.9 - - + -
196B PHE* 4.4 9.2 - - + -
198B VAL* 4.8 0.4 - - + -
226B PHE* 3.8 31.6 - - + +
228B ASP 3.1 23.2 + - - -
229B CYS 2.9 18.1 + - - +
231B ILE* 3.5 34.8 - - + -
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Residues in contact with ASN 161 (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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148B LYS 4.5 0.5 - - - +
149B LEU* 3.0 17.0 - - - +
150B LYS* 3.0 28.8 + - + +
152B GLU* 2.8 29.9 + - - +
159B ILE* 3.5 5.3 - - - +
160B LEU* 1.3 79.5 + - - +
162B GLY* 1.3 58.8 + - - +
226B PHE 3.4 4.1 - - - +
227B GLU* 3.7 4.9 - - - -
228B ASP* 3.0 41.9 + - - +
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Residues in contact with GLY 162 (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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148B LYS 5.4 1.1 - - - -
149B LEU* 4.2 10.1 - - - -
161B ASN* 1.3 75.8 - - - +
163B ASN* 1.3 62.5 + - - +
225B ILE* 3.8 2.3 - - - +
226B PHE* 2.8 36.4 + - - +
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Residues in contact with ASN 163 (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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137B GLU* 3.6 26.0 - - - +
138B PRO* 3.5 31.9 - - - +
149B LEU* 4.3 5.0 - - - +
162B GLY* 1.3 76.3 - - - +
164B LYS* 1.3 63.2 + - - +
223B GLU* 2.8 33.0 + - - +
224B LEU 2.8 20.2 - - - +
225B ILE* 4.3 6.1 - - + -
226B PHE* 4.7 2.2 - - - -
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Residues in contact with LYS 164 (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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134B ALA* 3.9 21.8 - - + -
135B MET* 2.9 25.7 + - - +
136B SER 3.3 13.9 - - - +
137B GLU* 3.0 20.6 + - + +
147B MET* 3.8 7.7 - - - -
149B LEU* 3.5 22.0 - - + -
163B ASN* 1.3 82.7 + - - +
165B PHE* 1.3 61.9 + - - +
167B ILE* 4.1 3.1 - - + -
178B VAL* 3.9 9.0 - - + -
179B TYR 2.9 29.6 + - - -
223B GLU* 3.3 12.0 - - - +
224B LEU* 2.9 48.6 + - + -
226B PHE* 4.5 0.7 - - + -
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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