Contacts of the strand formed by residues 217 - 223 (chain A) in PDB entry 3L4U
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 GLN 217 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180A LEU* 3.3 7.3 - - - -
181A GLY* 2.9 37.0 + - - +
182A GLU 4.9 0.2 - - - +
199A ILE* 4.0 5.2 - - - +
215A GLY 4.9 0.2 - - - -
216A ALA* 1.3 77.8 + - - +
218A THR* 1.3 61.1 + - - +
219A PHE 3.4 2.2 - - - +
277A TYR* 4.1 6.2 + - - -
528A THR* 3.0 28.5 + - - +
529A PHE 3.3 21.6 + - - -
530A ALA* 3.6 17.3 - - - +
531A GLY 5.2 0.2 - - - +
560A PHE* 4.4 6.0 - - + -
563A PHE* 3.6 55.9 - - + +
565A ILE* 4.0 10.5 - - - +
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Residues in contact with THR 218 (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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180A LEU* 3.6 10.1 - - - +
199A ILE* 4.5 10.3 - - + -
216A ALA* 4.4 2.0 + - + -
217A GLN* 1.3 77.2 - - - +
219A PHE* 1.3 61.3 + - - +
233A VAL 3.8 1.5 - - - +
234A PHE* 3.1 13.1 - - + -
235A LEU* 2.7 42.2 + - + +
237A ASN 4.5 4.5 - - - +
241A MET* 3.8 34.8 - - + -
253A TYR* 2.8 36.3 + - - -
529A PHE* 5.9 3.6 - - + -
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Residues in contact with PHE 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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179A GLY* 3.7 0.3 - - - -
180A LEU 2.9 26.4 + - - -
217A GLN* 3.4 3.0 - - - +
218A THR* 1.3 78.5 + - - +
220A PHE* 1.3 78.8 + - - +
221A LEU* 4.3 11.4 - - + -
232A GLY* 4.1 4.3 - - - -
233A VAL 3.3 19.1 - - - -
234A PHE* 4.1 3.5 - - + -
265A PHE* 4.0 14.1 - + - -
273A VAL* 3.9 19.1 - - + -
274A VAL* 4.9 4.3 - - + -
277A TYR* 3.6 66.2 - + + +
562A LEU* 4.0 28.9 - - + -
563A PHE* 3.5 20.9 - + + -
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Residues in contact with PHE 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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170A THR* 4.8 1.8 - - + -
172A LEU* 3.9 31.0 - - + -
177A VAL* 3.9 22.9 - - + -
178A TYR 3.2 15.7 - - - +
180A LEU* 4.1 12.8 - - + -
219A PHE* 1.3 82.1 - - - +
221A LEU* 1.3 65.9 + - - +
222A CYS* 4.3 12.8 - - + -
231A PHE* 4.6 3.4 - + - -
232A GLY* 3.1 4.2 - - - -
233A VAL* 3.1 63.8 + - + -
251A ILE* 3.8 27.8 - - + -
253A TYR* 3.2 29.2 - + - -
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Residues in contact with LEU 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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177A VAL* 3.5 4.0 - - - -
178A TYR* 2.8 55.5 + - + +
219A PHE* 4.3 9.6 - - + -
220A PHE* 1.3 78.8 - - - +
222A CYS* 1.3 76.2 + - - +
223A LEU* 4.1 3.1 - - + +
230A SER* 4.5 2.0 - - - +
231A PHE 3.5 9.9 - - - +
232A GLY* 4.2 0.9 - - - -
270A PRO* 3.5 46.2 - - + +
273A VAL* 4.0 12.3 - - + -
274A VAL* 3.7 20.6 - - + -
562A LEU* 4.3 6.5 - - + -
656A LEU* 5.5 0.2 - - + -
657A HIS* 4.3 9.9 - - + +
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Residues in contact with CYS 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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172A LEU* 5.1 1.1 - - - -
173A PRO* 3.9 17.0 - - - -
174A SER* 3.2 31.2 - - - -
176A ASN 3.3 7.4 - - - +
177A VAL* 4.5 6.3 - - + -
220A PHE* 4.3 9.6 + - + -
221A LEU* 1.3 78.8 - - - +
223A LEU* 1.3 60.3 + - - +
224A GLU 3.6 0.7 + - - -
230A SER* 3.1 5.9 - - - -
231A PHE* 2.8 69.6 + - + -
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Residues in contact with LEU 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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174A SER* 2.8 19.4 + - - -
176A ASN* 3.0 31.3 + - + +
178A TYR* 4.4 7.4 - - + -
221A LEU* 4.1 5.1 - - + +
222A CYS* 1.3 68.6 - - - +
224A GLU* 1.3 57.2 - - - +
225A ASP 3.2 22.9 - - - +
228A GLY* 3.6 19.5 - - - +
229A LEU 3.8 0.4 - - - +
230A SER* 3.5 19.7 - - - +
270A PRO* 4.1 4.5 - - + -
656A LEU* 4.2 15.5 - - + -
660A TYR* 4.0 16.6 - - + -
666A TRP* 3.5 45.8 - - + +
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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