Contacts of the strand formed by residues 157 - 164 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153C LYS* 3.4 5.0 - - - +
154C LYS* 2.7 41.8 + - + +
155C GLY 3.1 2.7 - - - +
156C ASN* 1.3 106.5 + - + +
158C TYR* 1.3 65.7 + - - +
159C ILE* 5.8 0.2 - - + -
230C LYS* 3.7 39.6 + - + +
231C ILE 3.2 7.9 - - - +
232C PRO* 3.4 24.6 - - + +
233C ALA 4.1 0.9 - - - +
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Residues in contact with TYR 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151C ALA* 3.7 17.0 - - + -
152C GLU 3.0 4.7 - - - +
153C LYS* 3.6 40.4 + - + +
155C GLY 5.6 0.2 - - - -
157C HIS* 1.3 78.5 - - - +
159C ILE* 1.3 64.0 + - - +
160C LEU* 3.9 9.6 - - + -
182C THR* 4.0 12.6 - - + -
194C THR* 5.9 0.2 - - + -
196C PHE* 3.6 37.2 - + + -
229C CYS 3.2 2.3 - - - +
230C LYS* 3.4 3.3 - - - -
231C ILE* 2.7 40.5 + - + +
233C ALA* 3.8 30.0 - - + +
236C ILE* 4.2 8.1 - - + +
240C GLU* 3.3 34.1 + - + +
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Residues in contact with ILE 159 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150C LYS 3.3 1.4 - - - +
152C GLU* 2.6 65.1 + - + +
154C LYS* 4.5 21.1 - - + -
158C TYR* 1.3 73.2 - - - +
160C LEU* 1.3 61.7 + - - +
161C ASN* 4.4 1.1 - - - +
228C ASP* 3.5 51.4 - - + +
229C CYS 3.4 1.1 - - - -
230C LYS* 3.3 40.4 - - + +
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Residues in contact with LEU 160 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149C LEU* 3.9 17.5 - - + -
150C LYS 3.3 2.5 - - - -
151C ALA* 3.4 28.5 - - + -
158C TYR* 4.2 14.8 - - + -
159C ILE* 1.3 74.6 - - - +
161C ASN* 1.3 60.7 + - - +
178C VAL* 4.6 10.3 - - + -
180C ALA* 4.7 1.3 - - + -
196C PHE* 4.4 15.3 - - + -
198C VAL* 4.7 0.7 - - + -
226C PHE* 3.7 34.6 - - + -
228C ASP* 3.0 24.1 + - - -
229C CYS 2.8 19.6 + - - +
231C ILE* 3.5 33.2 - - + -
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Residues in contact with ASN 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148C LYS 4.4 1.0 - - - +
149C LEU* 3.5 5.9 - - - +
150C LYS* 2.9 44.1 + - + +
152C GLU* 3.9 22.9 + - - +
160C LEU* 1.3 72.6 - - - +
162C GLY* 1.3 58.0 + - - +
226C PHE 3.4 2.4 - - - +
227C GLU* 3.5 5.7 - - - -
228C ASP* 2.7 47.9 + - - +
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Residues in contact with GLY 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148C LYS 5.4 1.8 - - - -
149C LEU* 4.5 10.3 - - - -
161C ASN* 1.3 75.6 - - - +
163C ASN* 1.3 62.0 + - - +
225C ILE* 3.9 1.7 - - - +
226C PHE* 2.8 34.4 + - - +
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Residues in contact with ASN 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137C GLU* 3.5 26.7 - - - +
138C PRO* 3.5 27.0 - - - +
149C LEU* 4.5 5.2 - - - +
162C GLY* 1.3 75.7 - - - +
164C LYS* 1.3 64.2 + - - +
223C GLU* 2.6 38.1 + - - +
224C LEU 2.8 17.7 - - - +
225C ILE* 4.3 6.1 - - + -
226C PHE* 4.7 2.0 - - - +
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Residues in contact with LYS 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134C ALA* 3.8 25.8 - - + -
135C MET 3.7 11.3 + - - +
136C SER 3.2 16.4 - - - +
137C GLU* 2.6 33.8 + - + +
147C MET* 4.0 4.6 - - - -
149C LEU* 3.4 20.7 - - + +
163C ASN* 1.3 76.2 - - - +
165C PHE* 1.3 61.8 + - - +
167C ILE* 4.1 6.5 - - + -
178C VAL* 3.8 9.0 - - + -
179C TYR 3.0 28.3 + - - -
223C GLU* 3.2 12.1 - - - +
224C LEU* 2.8 50.5 + - + +
226C PHE* 4.7 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