Contacts of the strand formed by residues 182 - 188 (chain A) in PDB entry 5E97
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 LEU 182 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176A PHE* 4.6 6.7 - - + -
177A ALA* 2.9 26.1 + - - +
178A ASN* 4.2 4.0 + - - +
180A SER* 3.7 27.8 - - - +
181A GLY* 1.3 88.4 - - - +
183A ASP* 1.3 64.7 + - - +
184A LEU 3.9 0.7 + - - -
385A PHE* 6.3 0.4 - - + -
59B VAL* 4.7 9.2 - - + -
84B ALA* 3.9 26.7 - - + +
87B LEU* 4.5 1.6 - - + -
88B SER* 4.1 8.1 - - - +
90B ALA* 3.3 30.5 - - + +
92B LEU* 4.1 34.1 - - + -
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Residues in contact with ASP 183 (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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181A GLY 5.0 2.8 - - - +
182A LEU* 1.3 73.9 - - - +
184A LEU* 1.3 64.9 + - - +
185A ILE 3.6 0.5 + - - -
217A ASN 6.0 0.4 - - - -
219A SER* 6.2 0.2 - - - +
55B SER* 4.7 6.6 + - - -
89B PRO* 5.6 2.4 - - - +
90B ALA 2.9 18.8 + - - +
91B TYR* 3.3 31.2 - - + -
92B LEU* 2.9 20.8 + - - +
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Residues in contact with LEU 184 (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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170A VAL* 5.6 1.3 - - + +
173A LEU* 3.9 43.7 - - + -
174A TYR* 4.2 24.2 - - + +
177A ALA* 4.2 11.9 - - + +
182A LEU 3.9 3.6 + - - -
183A ASP* 1.3 71.5 - - - +
185A ILE* 1.3 72.9 + - - +
186A PHE* 4.6 4.9 - - + +
217A ASN 4.7 5.8 + - - +
218A ILE* 3.8 34.7 - - + -
219A SER* 3.0 27.0 + - - +
92B LEU* 3.4 26.0 - - + +
94B PHE* 4.2 4.5 - - + -
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Residues in contact with ILE 185 (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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183A ASP 4.3 0.9 - - - +
184A LEU* 1.3 78.0 - - - +
186A PHE* 1.3 60.5 + - - +
219A SER* 3.3 19.1 - - - +
220A TRP 4.3 0.2 - - - -
221A GLU* 3.5 37.5 - - + +
264A TYR* 3.9 21.5 - - + -
340A TRP* 4.2 0.7 - - + -
381A MET* 3.5 34.1 - - + -
91B TYR* 3.6 31.9 - - + -
92B LEU 2.9 7.1 + - - +
93B ARG* 4.1 9.4 - - + +
94B PHE* 2.8 33.6 + - - +
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Residues in contact with PHE 186 (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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165A TYR* 3.6 33.7 - + - -
170A VAL* 5.0 12.3 - - + -
173A LEU* 3.7 24.0 - - + -
184A LEU* 4.1 7.2 - - + -
185A ILE* 1.3 73.4 - - - +
187A GLY* 1.3 80.3 + - - +
188A LEU* 3.5 5.0 + - + -
207A LEU* 3.6 19.3 - - + -
218A ILE* 3.8 13.0 - - + -
219A SER 2.8 9.1 + - - -
220A TRP* 3.5 35.6 - + + -
221A GLU* 3.0 20.9 + - - +
94B PHE* 3.6 28.0 - + - -
102B LEU* 6.2 0.4 - - + -
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Residues in contact with GLY 187 (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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185A ILE 4.1 0.4 + - - -
186A PHE* 1.3 89.4 - - - +
188A LEU* 1.3 62.1 + - - -
189A ASN 4.1 0.5 + - - -
221A GLU* 3.7 21.0 + - - +
223A GLY 5.8 0.2 - - - -
93B ARG* 6.0 0.7 - - - -
94B PHE* 3.0 22.7 + - - +
95B GLY* 5.2 0.4 - - - -
99B THR* 3.6 23.4 + - - +
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Residues in contact with LEU 188 (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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165A TYR* 5.1 2.2 - - - +
186A PHE* 4.1 4.3 - - + -
187A GLY* 1.3 73.0 - - - -
189A ASN* 1.3 62.1 + - - +
190A ALA 3.2 0.2 + - - -
199A TRP* 4.8 4.9 - - + -
204A ALA* 4.1 25.8 - - + +
207A LEU* 3.7 30.1 - - + -
208A LEU* 5.1 3.1 - - + -
220A TRP* 3.9 27.4 - - + -
221A GLU 2.8 17.4 + - - +
222A LEU* 3.7 11.1 - - + -
223A GLY 2.9 26.0 + - - -
249A LEU* 3.8 38.6 - - + -
99B THR* 3.2 7.1 - - - +
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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