Contacts of the strand formed by residues 218 - 225 (chain A) in PDB entry 4WLQ
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 PHE 218 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A TRP* 6.1 1.1 - + - -
54A PHE* 4.1 11.9 - + + -
55A LEU* 3.1 17.3 - - - +
56A PHE* 3.7 12.6 - - + +
163A PHE* 5.4 1.3 - - - -
208A ILE* 3.5 55.4 - - + -
211A TYR* 3.8 12.1 - - + -
212A SER* 4.1 17.7 - - - -
216A ILE 3.2 22.2 - - - +
217A ARG* 1.3 75.9 - - - +
219A ASN* 1.3 73.0 + - - +
220A LEU* 5.1 1.1 - - + -
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Residues in contact with ASN 219 (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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13A SER* 5.2 4.8 + - - -
34A GLU* 2.7 31.4 + - - +
35A ILE 4.6 1.0 - - - +
36A TRP* 3.9 15.0 - - - -
54A PHE* 4.1 1.2 - - - -
55A LEU* 2.6 60.5 + - + +
218A PHE* 1.3 85.9 - - - +
220A LEU* 1.3 77.6 + - - +
221A MET* 3.3 24.9 - - - +
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Residues in contact with LEU 220 (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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34A GLU* 3.7 0.7 - - - +
35A ILE* 3.2 47.4 + - + +
38A LEU* 5.2 12.3 - - + -
43A PHE* 5.8 0.7 - - + -
52A LEU* 3.9 22.2 - - + -
53A ILE 3.4 19.7 - - - +
54A PHE* 4.0 15.0 - - + -
204A ILE* 3.5 36.6 - - + -
208A ILE* 5.0 11.0 - - + -
218A PHE* 5.1 1.3 - - + -
219A ASN* 1.3 87.9 + - - +
221A MET* 1.3 74.5 + - - +
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Residues in contact with MET 221 (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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13A SER* 4.2 14.8 - - - +
14A ASP* 4.2 2.9 - - - +
15A PRO* 4.3 11.0 - - + -
18A PHE* 3.7 35.2 - - + -
32A VAL* 4.2 12.3 - - + -
33A GLU 3.3 7.2 - - - +
34A GLU* 3.7 21.1 - - + -
35A ILE* 4.3 5.6 - - - +
52A LEU* 3.2 7.6 - - - +
53A ILE* 2.8 44.2 + - + +
55A LEU* 4.0 19.7 - - + -
219A ASN* 3.3 27.1 - - - +
220A LEU* 1.3 83.3 - - - +
222A ALA* 1.3 63.0 + - - +
223A ILE* 5.8 0.2 - - - -
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Residues in contact with ALA 222 (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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32A VAL* 3.2 6.7 - - - +
33A GLU* 2.7 37.3 + - + +
35A ILE* 3.7 27.6 - - + -
43A PHE* 5.3 0.7 - - + -
46A LEU* 5.1 1.3 - - + -
49A VAL* 4.1 4.0 - - + -
51A GLY 3.5 4.0 - - - -
52A LEU* 3.8 12.8 - - + -
221A MET* 1.3 78.0 - - - +
223A ILE* 1.3 62.8 + - - +
224A VAL* 3.4 18.5 + - + +
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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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22A ILE* 4.4 19.5 - - + -
30A ALA* 4.2 20.0 - - + -
31A GLN 3.5 9.6 - - - +
32A VAL* 4.3 9.2 - - + +
49A VAL* 3.7 1.0 - - - +
50A HIS* 2.7 42.0 + - + +
51A GLY 2.9 18.8 + - - +
53A ILE* 3.7 28.7 - - + -
93A ILE* 4.3 10.1 - - + +
96A VAL* 3.6 29.8 - - + -
97A LEU* 4.6 10.5 - - + -
222A ALA* 1.3 71.8 - - - +
224A VAL* 1.3 55.1 + - - +
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Residues in contact with VAL 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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30A ALA* 3.3 5.2 - - - +
31A GLN* 2.9 50.1 + - + +
33A GLU* 4.2 11.2 - - + -
46A LEU* 3.4 36.6 - - + +
48A PRO 3.3 12.3 - - - +
49A VAL* 4.1 13.0 - - + -
50A HIS* 3.6 6.1 - - - -
222A ALA* 3.4 13.0 + - + +
223A ILE* 1.3 78.3 - - - +
225A SER* 1.3 71.2 + - - +
227A ARG* 4.1 11.9 - - - +
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Residues in contact with SER 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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29A GLY 3.3 9.4 - - - -
31A GLN* 3.9 0.6 - - - +
48A PRO* 3.2 23.6 + - - +
50A HIS* 2.8 25.3 + - - -
104A ASP* 2.7 33.0 + - - +
224A VAL* 1.3 91.7 - - - +
226A ASP* 1.3 61.4 + - - +
227A ARG* 3.1 15.2 + - - -
230A ILE* 4.1 9.4 - - - -
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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