Contacts of the strand formed by residues 222 - 229 (chain A) in PDB entry 1SEE
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 222 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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231 ZN 2.3 32.0 - - - -
124A ILE* 4.6 6.3 - - - -
125A ASN* 3.3 35.5 - - + +
184A HIS* 2.8 44.5 + - + +
220A ASN 5.2 0.7 - - - +
221A LEU* 1.3 78.1 - - - +
223A ILE* 1.3 88.5 + - - +
224A ASP* 3.3 10.8 - - - -
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Residues in contact with ILE 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A ILE* 3.3 41.8 - - + +
125A ASN 2.7 39.3 + - - +
139A LYS 5.6 0.2 - - - +
152A LEU* 3.9 12.3 - - + -
156A ALA* 4.7 5.4 - - + -
181A ILE* 3.5 29.8 - - + -
182A VAL 3.1 13.7 - - - +
183A PHE* 3.9 22.7 - - + -
184A HIS* 3.6 1.1 - - - -
221A LEU* 3.5 28.9 - - + -
222A HIS* 1.3 80.8 - - - +
224A ASP* 1.3 63.5 - - - +
225A LEU* 5.3 1.3 - - + -
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Residues in contact with ASP 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231 ZN 2.6 33.4 - - - -
125A ASN* 2.6 29.5 - - - +
127A TRP* 3.1 24.5 + - + -
182A VAL* 2.8 45.4 + - + +
184A HIS* 2.6 4.0 + - - -
222A HIS* 3.3 4.5 - - - -
223A ILE* 1.3 75.4 - - - +
225A LEU* 1.3 58.7 + - - +
226A TYR* 4.0 19.0 + - + +
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Residues in contact with LEU 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A ASN 4.0 0.6 + - - -
126A LEU* 3.0 37.7 - - + +
127A TRP* 3.3 15.4 + - - +
156A ALA* 5.1 1.1 - - + +
160A LEU* 3.3 34.5 - - + -
180A LEU 3.1 28.0 - - - +
181A ILE* 4.0 12.1 - - + -
195A LEU* 3.6 22.9 - - + -
223A ILE* 5.3 1.6 - - + -
224A ASP* 1.3 75.7 - - - +
226A TYR* 1.3 85.5 + - - +
227A LEU* 3.4 25.8 - - + -
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Residues in contact with TYR 226 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A GLU* 4.4 21.2 + - + -
9A LEU* 5.5 0.2 - - - +
127A TRP* 3.8 32.9 - + + -
129A ASP 5.2 7.9 - - - +
178A ARG* 4.1 9.9 + - - +
179A GLY* 3.2 22.7 - - - -
180A LEU* 3.1 40.1 + - + +
182A VAL* 3.6 23.7 - - + +
224A ASP* 4.0 20.5 + - + +
225A LEU* 1.3 80.6 - - - +
227A LEU* 1.3 61.9 + - - +
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Residues in contact with LEU 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A LEU* 4.5 7.0 - - + -
127A TRP 3.4 8.2 + - - +
128A ILE* 3.3 16.7 - - + +
129A ASP* 2.8 26.7 + - - +
160A LEU* 4.6 4.0 - - + -
164A PHE* 3.9 33.7 - - + -
166A LEU* 3.6 25.6 - - + -
176A VAL* 3.5 22.9 - - + -
178A ARG* 3.5 2.0 - - - -
179A GLY* 4.1 9.2 - - - -
195A LEU* 4.6 0.9 - - + -
196A PHE* 4.5 1.1 - - + -
225A LEU* 3.4 35.2 - - + -
226A TYR* 1.3 74.0 - - - +
228A TYR* 1.3 59.9 + - - +
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Residues in contact with TYR 228 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129A ASP* 4.6 14.8 - - + +
176A VAL* 3.0 5.2 - - - +
177A GLN* 2.6 57.8 + - - -
178A ARG* 2.9 63.5 + - + +
227A LEU* 1.3 73.9 - - - +
229A THR* 1.3 74.1 + - - +
230A THR* 5.7 0.4 - - - -
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Residues in contact with THR 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A ILE* 3.2 27.1 - - + +
129A ASP* 5.0 5.0 - - - +
175A LYS* 3.2 25.6 - - + +
176A VAL* 4.0 2.2 - - + +
177A GLN* 3.6 3.2 + - - -
228A TYR* 1.3 97.5 - - - +
230A THR* 1.4 75.5 + - + +
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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