Contacts of the strand formed by residues 194 - 203 (chain B) in PDB entry 1YI5
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 ASP 194 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89B TYR* 4.6 18.4 - - + +
139B LYS* 3.7 23.0 + - + +
140B ILE 3.7 13.2 - - - +
141B GLY* 3.9 8.5 - - - -
152B VAL* 3.9 6.8 - - - +
180B LYS* 5.0 0.9 - - - +
181B ASN* 2.5 59.8 + - - +
183B VAL* 3.9 10.2 - - - +
192B TYR 3.9 8.6 - - - +
193B GLU* 1.3 78.4 - - - +
195B VAL* 1.3 63.2 + - - +
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Residues in contact with VAL 195 (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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31B VAL* 4.8 17.9 - - + -
86B LEU* 6.3 0.7 - - + -
139B LYS* 3.6 3.0 - - - +
140B ILE* 2.8 52.5 + - + +
152B VAL* 3.5 29.1 - - + +
154B PRO* 4.2 38.4 - - + -
178B GLN* 4.5 4.9 - - + +
179B LYS 4.8 1.8 - - - +
180B LYS* 4.5 4.7 - - + +
194B ASP* 1.3 72.4 - - - +
196B GLU* 1.3 71.5 + - - +
197B VAL* 4.0 14.6 - - + -
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Residues in contact with GLU 196 (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 ARG* 3.9 34.5 + - + -
138B ILE 3.8 7.6 - - - +
139B LYS* 4.0 31.9 + - + +
177B THR 3.8 2.1 - - - +
179B LYS* 3.2 43.0 + - - +
181B ASN* 4.7 10.4 + - + -
194B ASP 3.9 0.8 + - - -
195B VAL* 1.3 75.5 - - - +
197B VAL* 1.3 69.0 + - - +
198B SER* 3.9 12.7 + - - +
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Residues in contact with VAL 197 (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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33B LEU* 4.0 27.4 - - + -
35B PHE* 3.8 29.6 - - + -
136B CYS 3.7 2.4 - - - +
137B ARG* 3.8 2.3 - - - -
138B ILE* 3.0 39.2 + - + +
140B ILE* 4.9 4.9 - - + -
176B VAL* 4.1 19.1 - - + -
177B THR 3.8 2.7 - - - -
178B GLN* 4.0 23.6 - - + +
195B VAL* 4.2 10.8 - - + -
196B GLU* 1.3 76.3 - - - +
198B SER* 1.3 64.9 + - - +
199B LEU* 3.9 0.4 - - - +
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Residues in contact with SER 198 (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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135B THR* 5.1 11.3 - - - +
136B CYS 3.9 4.7 - - - +
137B ARG* 4.0 17.5 + - - +
175B ASP 3.5 4.2 - - - +
176B VAL* 3.3 7.3 - - - -
177B THR* 2.9 50.5 + - - +
196B GLU* 3.9 16.6 + - - +
197B VAL* 1.3 77.0 + - - +
199B LEU* 1.3 60.6 + - - +
200B ASN 3.5 0.8 + - - -
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Residues in contact with LEU 199 (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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35B PHE* 3.3 59.5 - - + -
38B ILE* 4.0 10.3 - - + -
48B VAL* 5.7 2.9 - - + -
50B VAL* 5.0 2.9 - - + -
134B ALA 3.6 2.1 - - - +
135B THR* 4.4 0.7 - - - -
136B CYS* 2.8 52.0 + - + +
138B ILE* 5.6 1.1 - - + -
173B ILE* 4.2 13.7 - - + -
176B VAL* 3.5 18.2 - - + -
197B VAL* 3.9 1.2 + - + +
198B SER* 1.3 70.0 - - - +
200B ASN* 1.3 62.0 + - - +
201B PHE* 3.4 32.3 - - + -
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Residues in contact with ASN 200 (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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132B SER 3.2 26.4 + - - +
133B GLY 3.8 2.4 - - - -
134B ALA 3.2 11.8 - - - +
135B THR* 4.2 22.3 + - + +
173B ILE* 3.9 5.5 - - - +
174B LEU* 3.1 32.4 + - - +
175B ASP* 3.1 32.6 + - + +
198B SER 3.5 2.2 + - - +
199B LEU* 1.3 72.7 - - - +
201B PHE* 1.3 70.4 + - - +
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Residues in contact with PHE 201 (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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38B ILE* 3.8 24.9 - - + -
41B VAL* 4.5 20.0 - - + -
48B VAL* 4.3 21.1 - - + -
125B VAL* 5.3 2.5 - - + -
128B VAL* 4.7 14.6 - - + -
133B GLY* 3.3 4.0 - - - -
134B ALA* 2.9 45.9 + - + +
136B CYS* 3.6 26.5 - - + -
171B PHE* 4.5 9.9 - + + -
172B GLU 3.8 13.0 - - - +
173B ILE* 4.4 4.5 - - + -
174B LEU* 4.4 4.9 - - - +
199B LEU* 3.4 32.3 - - + -
200B ASN* 1.3 76.6 + - - +
202B ARG* 1.3 70.8 + - - +
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Residues in contact with ARG 202 (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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128B VAL* 3.6 16.8 - - - +
130B THR 3.6 13.0 + - - +
131B GLU* 4.1 39.5 + - - +
133B GLY* 3.9 10.5 - - - -
171B PHE* 3.1 16.2 - - - +
172B GLU* 3.1 59.5 + - + +
174B LEU* 4.0 18.6 - - + +
201B PHE* 1.3 84.2 - - - +
203B LYS* 1.3 73.5 + - - +
204B LYS* 5.8 1.4 - - - +
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Residues in contact with LYS 203 (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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128B VAL* 3.5 22.5 + - + +
129B ASP* 4.4 24.7 - - + +
130B THR 5.4 0.5 - - - +
170B ARG* 3.1 51.4 - - + +
171B PHE* 3.9 14.8 - - + -
172B GLU* 5.0 0.9 - - - -
202B ARG* 1.3 96.4 + - - +
204B LYS* 1.3 73.6 + - - +
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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