Contacts of the strand formed by residues 273 - 279 (chain D) in PDB entry 4WLE
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 VAL 273 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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257D ARG* 5.2 1.7 + - - -
271D GLY* 3.3 12.7 + - - +
272D VAL* 1.3 79.5 - - - +
274D GLU* 1.3 74.4 + - - +
291D PRO* 3.8 19.7 - - + -
292D LEU 3.3 6.1 - - - +
293D LEU* 3.8 17.0 - - + -
303D LEU* 3.8 29.8 - - + -
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Residues in contact with GLU 274 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171D THR* 4.4 8.3 + - - +
174D ILE* 5.5 2.6 - - - +
257D ARG* 3.0 46.9 + - - +
258D PHE* 4.0 28.0 - - + -
261D SER* 2.8 39.7 + - - +
272D VAL* 4.3 1.3 - - + -
273D VAL* 1.3 80.1 - - - +
275D CYS* 1.3 66.4 + - - +
276D SER* 4.6 0.5 - - - -
291D PRO* 4.2 1.8 - - - -
292D LEU* 2.9 35.2 + - - +
294D LEU* 4.3 10.2 - - + +
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Residues in contact with CYS 275 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170D THR* 3.5 8.2 + - - -
171D THR* 4.4 9.2 + - - -
174D ILE* 3.7 21.7 - - + +
195D PRO* 4.1 6.5 - - - -
196D VAL 3.4 41.3 - - - +
258D PHE* 4.3 3.6 - - - -
274D GLU* 1.3 81.7 + - - +
276D SER* 1.3 62.2 + - - +
289D SER* 4.2 2.7 - - - +
290D THR 3.4 8.3 - - - +
291D PRO* 3.8 30.3 - - - -
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Residues in contact with SER 276 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167D PHE* 3.5 23.8 - - - +
168D GLY 2.8 19.4 + - - -
170D THR* 3.6 6.1 - - - -
258D PHE* 3.8 19.6 - - - -
274D GLU 3.7 0.8 + - - -
275D CYS* 1.3 77.7 - - - +
277D PHE* 1.3 61.3 + - - +
278D VAL* 3.3 11.5 + - - +
288D PHE 3.7 1.4 - - - +
289D SER* 3.3 21.3 + - - -
290D THR 3.4 9.8 + - - +
292D LEU* 4.0 16.2 - - - +
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Residues in contact with PHE 277 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144D VAL* 3.8 24.0 - - + -
145D ASN* 3.8 28.9 - - - -
148D ILE* 3.8 25.8 - - + +
149D PRO* 4.1 0.9 - - + -
167D PHE* 3.8 0.5 - - - -
168D GLY* 2.8 45.8 + - - +
170D THR* 3.9 13.6 - - + +
198D GLY 3.3 27.1 - - - -
199D GLY* 4.0 6.5 - - - -
276D SER* 1.3 67.3 - - - +
278D VAL* 1.3 59.8 + - - +
287D TYR* 3.5 31.2 - - + -
288D PHE* 3.7 12.8 - - - -
289D SER* 3.6 9.2 + - - -
323D LEU* 4.0 11.4 - - + -
327D ILE* 4.6 3.8 - - + -
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Residues in contact with VAL 278 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148D ILE* 4.9 1.6 - - - -
163D PRO 5.0 0.2 - - - +
166D ILE 3.5 21.5 - - - +
167D PHE* 3.8 11.0 - - + -
276D SER* 3.7 11.2 - - - +
277D PHE* 1.3 80.9 - - - +
279D LYS* 1.3 75.2 + - - +
287D TYR* 3.2 9.4 - - - -
288D PHE 2.9 35.1 + - - +
292D LEU* 3.6 41.1 - - + -
299D ILE* 3.8 16.8 - - + -
302D ASN* 4.3 5.2 - - - +
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Residues in contact with LYS 279 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148D ILE* 5.3 0.6 - - - +
156D LYS* 5.9 4.0 - - - +
161D TYR* 3.5 30.1 - - + +
163D PRO* 3.9 24.6 + - + +
166D ILE 5.1 1.0 + - - -
278D VAL* 1.3 82.1 - - - +
280D SER* 1.3 64.6 + - - +
281D GLN* 3.0 32.5 + - - +
286D THR* 3.0 40.0 + - - +
287D TYR* 3.6 23.0 - - + +
299D ILE* 5.3 2.3 - - - +
302D ASN* 4.5 3.1 + - - -
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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